diff --git a/variation-commons-batch/src/main/java/uk/ac/ebi/eva/commons/batch/io/AggregatedVcfLineMapper.java b/variation-commons-batch/src/main/java/uk/ac/ebi/eva/commons/batch/io/AggregatedVcfLineMapper.java
index 558060c4..b20ec3e5 100644
--- a/variation-commons-batch/src/main/java/uk/ac/ebi/eva/commons/batch/io/AggregatedVcfLineMapper.java
+++ b/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);
}
}
diff --git a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/IVariantSource.java b/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/IVariantSource.java
index 51d9dc93..94ae64d0 100644
--- a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/IVariantSource.java
+++ b/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);
}
diff --git a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/VariantSource.java b/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/VariantSource.java
index 72381ff3..3f813d37 100644
--- a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/VariantSource.java
+++ b/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;
diff --git a/variation-commons-mongodb/pom.xml b/variation-commons-mongodb/pom.xml
index 0fe57b90..5a8853d4 100644
--- a/variation-commons-mongodb/pom.xml
+++ b/variation-commons-mongodb/pom.xml
@@ -35,6 +35,11 @@
variation-commons-core
0.7-SNAPSHOT
+
+ uk.ac.ebi.eva
+ biodata-models
+ 0.4.7
+
diff --git a/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/VariantSourceMongo.java b/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/VariantSourceMongo.java
index 8869c309..2d5582d3 100644
--- a/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/VariantSourceMongo.java
+++ b/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);
+ }
+
}
diff --git a/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/projections/SimplifiedVariant.java b/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/projections/SimplifiedVariant.java
index ebdac378..303eee96 100644
--- a/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/projections/SimplifiedVariant.java
+++ b/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;
+ }
}
diff --git a/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/subdocuments/ConsequenceTypeMongo.java b/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/subdocuments/ConsequenceTypeMongo.java
index f5e502dd..de4540f3 100644
--- a/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/entities/subdocuments/ConsequenceTypeMongo.java
+++ b/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);
}
diff --git a/variation-commons-mongodb/src/test/resources/test-mongo.properties b/variation-commons-mongodb/src/test/resources/test-mongo.properties
index 0a53861f..fa6ae22e 100644
--- a/variation-commons-mongodb/src/test/resources/test-mongo.properties
+++ b/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
\ No newline at end of file
+spring.data.mongodb.authentication-database=admin
+spring.data.mongodb.username=appAdmin
+spring.data.mongodb.password=password
\ No newline at end of file