Merge pull request #25 from jmmut/feature/reduce-document

EVA-1251 Reduce size of MongoDB documents
EBIvariation · Jun 19, 2018 · 61f2782 · 61f2782
2 parents 5442086 + a684516
commit 61f2782
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Showing 3 changed files with 19 additions and 0 deletions.
diff --git a/...ion-core/src/main/java/uk/ac/ebi/eva/accession/core/configuration/MongoConfiguration.java b/...ion-core/src/main/java/uk/ac/ebi/eva/accession/core/configuration/MongoConfiguration.java
@@ -27,7 +27,11 @@
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 import org.springframework.core.env.Environment;
+import org.springframework.data.mongodb.MongoDbFactory;
 import org.springframework.data.mongodb.config.EnableMongoAuditing;
+import org.springframework.data.mongodb.core.MongoTemplate;
+import org.springframework.data.mongodb.core.convert.DefaultMongoTypeMapper;
+import org.springframework.data.mongodb.core.convert.MappingMongoConverter;
 import org.springframework.data.mongodb.repository.config.EnableMongoRepositories;
 
 import java.net.UnknownHostException;
@@ -56,4 +60,10 @@ public MongoClient mongoClient(MongoProperties properties, ObjectProvider<MongoC
         return properties.createMongoClient(mongoClientOptions, environment);
     }
 
+    @Bean
+    public MongoTemplate mongoTemplate(MongoDbFactory mongoDbFactory,
+                                       MappingMongoConverter converter) throws UnknownHostException {
+        converter.setTypeMapper(new DefaultMongoTypeMapper(null));
+        return new MongoTemplate(mongoDbFactory, converter);
+    }
 }
diff --git a/...n-core/src/main/java/uk/ac/ebi/eva/accession/core/persistence/SubmittedVariantEntity.java b/...n-core/src/main/java/uk/ac/ebi/eva/accession/core/persistence/SubmittedVariantEntity.java
@@ -18,6 +18,7 @@
 package uk.ac.ebi.eva.accession.core.persistence;
 
 import org.springframework.data.mongodb.core.mapping.Document;
+import org.springframework.data.mongodb.core.mapping.Field;
 import uk.ac.ebi.ampt2d.commons.accession.persistence.mongodb.document.AccessionedDocument;
 
 import uk.ac.ebi.eva.accession.core.ISubmittedVariant;
@@ -27,20 +28,26 @@
 @Document
 public class SubmittedVariantEntity extends AccessionedDocument<Long> implements ISubmittedVariant {
 
+    @Field("asm")
     private String assemblyAccession;
 
+    @Field("tax")
     private int taxonomyAccession;
 
+    @Field("study")
     private String projectAccession;
 
     private String contig;
 
     private long start;
 
+    @Field("ref")
     private String referenceAllele;
 
+    @Field("alt")
     private String alternateAllele;
 
+    @Field("evidence")
     private boolean supportedByEvidence;
 
     SubmittedVariantEntity() {

diff --git a/...ssion-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/io/AccessionWriterTest.java b/...ssion-pipeline/src/test/java/uk/ac/ebi/eva/accession/pipeline/io/AccessionWriterTest.java
@@ -177,11 +177,13 @@ public void testSaveInitializesCreatedDate() throws Exception {
                                                         "reference", "alternate", false);
         LocalDateTime beforeSave = LocalDateTime.now();
         accessionWriter.write(Collections.singletonList(variant));
+        LocalDateTime afterSave = LocalDateTime.now();
 
         List<AccessionWrapper<ISubmittedVariant, String, Long>> accessions = service.get(Collections.singletonList(variant));
         assertEquals(1, accessions.size());
         ISubmittedVariant savedVariant = accessions.iterator().next().getData();
         assertTrue(beforeSave.isBefore(savedVariant.getCreatedDate()));
+        assertTrue(afterSave.isAfter(savedVariant.getCreatedDate()));
     }
 
     @Test