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