Update models wrt eva-pipeline issue #147

variation-commons-batch/src/main/java/uk/ac/ebi/eva/commons/batch/io/AggregatedVcfLineMapper.java

@@ -73,7 +73,7 @@ public AggregatedVcfLineMapper(String fileId, String studyId, Aggregation aggreg
             default:
                 throw new IllegalArgumentException(
                         this.getClass().getSimpleName() + " should be used to read aggregated VCFs only, " +
-                                "but the VariantSource.Aggregation is set to " + aggregation);
+                                "but the Aggregation is set to " + aggregation);
         }
     }
 

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

@@ -40,4 +40,5 @@ public interface IVariantSource {
 
     IVariantGlobalStats getStats();
 
+    void addMetadata(String key, Object value);
 }

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

@@ -18,6 +18,7 @@
 import uk.ac.ebi.eva.commons.core.models.stats.VariantGlobalStats;
 
 import java.util.Date;
+import java.util.HashMap;
 import java.util.Map;
 
 /**
@@ -75,7 +76,7 @@ public VariantSource(String fileId, String fileName, String studyId, String stud
         this.aggregation = aggregation;
         this.date = date;
         this.samplesPosition = samplesPosition;
-        this.metadata = metadata;
+        this.metadata = (metadata != null) ? metadata : new HashMap<>();
         if (stats != null) {
             this.stats = new VariantGlobalStats(stats);
         }
@@ -131,6 +132,11 @@ public VariantGlobalStats getStats() {
         return stats;
     }
 
+    @Override
+    public void addMetadata(String key, Object value) {
+        this.metadata.put(key, value);
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;

variation-commons-mongodb/pom.xml

@@ -35,6 +35,11 @@
             <artifactId>variation-commons-core</artifactId>
             <version>0.7-SNAPSHOT</version>
         </dependency>
+        <dependency>
+            <groupId>uk.ac.ebi.eva</groupId>
+            <artifactId>biodata-models</artifactId>
+            <version>0.4.7</version>
+        </dependency>
     </dependencies>
 
 

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

@@ -183,4 +183,9 @@ public void setStats(VariantGlobalStatsMongo stats) {
         this.stats = stats;
     }
 
+    @Override
+    public void addMetadata(String key, Object value) {
+        this.metadata.put(key, value);
+    }
+
 }

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

@@ -94,4 +94,23 @@ public SimplifiedVariant(VariantType variantType, String chromosome, long start,
         }
     }
 
+    public String getChromosome() {
+        return chromosome;
+    }
+
+    public int getStart() {
+        return (int) start;
+    }
+
+    public int getEnd() {
+        return (int) end;
+    }
+
+    public String getReference() {
+        return reference;
+    }
+
+    public String getAlternate() {
+        return alternate;
+    }
 }

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/test/resources/test-mongo.properties

@@ -1,5 +1,5 @@
 ## spring.data.mongodb.database
 spring.data.mongodb.host=localhost:27017
-#spring.data.mongodb.authentication-database
-#spring.data.mongodb.username
-#spring.data.mongodb.password
+spring.data.mongodb.authentication-database=admin
+spring.data.mongodb.username=appAdmin
+spring.data.mongodb.password=password