Merge pull request #93 from sundarvenkata-EBI/ops/spring2_upgrade

EVA-1905 - Spring 2 upgrade

Author: sundarvenkata-EBI

.travis.yml

@@ -4,9 +4,19 @@ dist: xenial
 
 language: java
 
-jdk:
-  - openjdk8
+matrix:
+  include:
+    - language: "java"
+      jdk: openjdk8
+      env:
+        - OPENCGA_HOME=$TRAVIS_BUILD_DIR/opencga/opencga-app/build
+        - MONGODB_VERSION=4.0.18
+      install:
+        - wget http://fastdl.mongodb.org/linux/mongodb-linux-x86_64-$MONGODB_VERSION.tgz
+        - tar xfz mongodb-linux-x86_64-$MONGODB_VERSION.tgz
+        - export PATH=`pwd`/mongodb-linux-x86_64-$MONGODB_VERSION/bin:$PATH
+        - mkdir -p data/db
+        - mongod --dbpath=data/db &
+        - mongod --version
 
-env:
-  - OPENCGA_HOME=$TRAVIS_BUILD_DIR/opencga/opencga-app/build
 

pom.xml

@@ -18,7 +18,7 @@
 
     <properties>
         <java.version>1.8</java.version>
-        <spring.boot.version>1.4.2.RELEASE</spring.boot.version>
+        <spring.boot.version>2.1.0.RELEASE</spring.boot.version>
     </properties>
 
     <dependencyManagement>
@@ -43,12 +43,6 @@
                 <scope>test</scope>
                 <version>0.14.0</version>
             </dependency>
-            <dependency>
-                <groupId>com.github.fakemongo</groupId>
-                <artifactId>fongo</artifactId>
-                <scope>test</scope>
-                <version>2.1.0</version>
-            </dependency>
             <dependency>
                 <groupId>javax.validation</groupId>
                 <artifactId>validation-api</artifactId>
@@ -75,7 +69,6 @@
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-mongodb</artifactId>
-            <version>1.4.2.RELEASE</version>
         </dependency>
 
         <dependency>

variation-commons-jpa/src/test/java/uk/ac/ebi/eva/commons/jpa/models/metadata/database/FileDatabaseTest.java

@@ -19,7 +19,7 @@
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.orm.jpa.JpaSystemException;
+import org.springframework.dao.DataIntegrityViolationException;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
@@ -132,7 +132,7 @@ public void testDelete() {
      *
      * @todo How to report this kind of errors?
      */
-    @Test(expected = JpaSystemException.class)
+    @Test(expected = DataIntegrityViolationException.class)
     public void testUpdateDuplicate() {
         File savedFile1 = repository.save(file1);
         File savedFile2 = repository.save(file2);

variation-commons-jpa/src/test/java/uk/ac/ebi/eva/commons/jpa/models/metadata/database/OrganisationDatabaseTest.java

@@ -19,7 +19,7 @@
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.orm.jpa.JpaSystemException;
+import org.springframework.dao.DataIntegrityViolationException;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
@@ -154,7 +154,7 @@ public void testUpdateNonDuplicate() {
      *
      * @todo How to report this kind of errors?
      */
-    @Test(expected = JpaSystemException.class)
+    @Test(expected = DataIntegrityViolationException.class)
     public void testUpdateDuplicate() {
         Organisation savedOrganisation1 = repository.save(organisation1);
         Organisation savedOrganisation2 = repository.save(organisation2);

variation-commons-jpa/src/test/java/uk/ac/ebi/eva/commons/jpa/models/metadata/database/PublicationDatabaseTest.java

@@ -4,7 +4,7 @@
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.orm.jpa.JpaSystemException;
+import org.springframework.dao.DataIntegrityViolationException;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.transaction.annotation.Transactional;
@@ -192,7 +192,7 @@ public void testUpdateNonDuplicate() {
      *
      * @todo How to report this kind of errors?
      */
-    @Test(expected = JpaSystemException.class)
+    @Test(expected = DataIntegrityViolationException.class)
     public void testUpdateDuplicate() {
         Publication savedPublication1 = repository.save(publication1);
         Publication savedPublication3 = repository.save(publication3);

variation-commons-jpa/src/test/java/uk/ac/ebi/eva/commons/jpa/models/metadata/database/StudyDatabaseTest.java

@@ -30,12 +30,15 @@
 import uk.ac.ebi.eva.commons.jpa.models.metadata.Organisation;
 import uk.ac.ebi.eva.commons.jpa.models.metadata.Study;
 
+import java.util.Optional;
+
 import static org.hamcrest.Matchers.containsInAnyOrder;
 import static org.hamcrest.Matchers.empty;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
 
 @RunWith(SpringJUnit4ClassRunner.class)
 @Transactional
@@ -207,11 +210,13 @@ public void addOneAnalisysToManyStudies() {
         assertEquals(study2, savedStudy2);
 
         // check that just study2 has a file generator, and that file generator is the analysis 1
-        Study studyFromRepository1 = repository.findOne(savedStudy1.getId());
-        Study studyFromRepository2 = repository.findOne(savedStudy2.getId());
-        assertEquals(studyFromRepository1.getFileGenerators().size(), 0);
-        assertEquals(studyFromRepository2.getFileGenerators().size(), 1);
-        assertEquals(studyFromRepository2.getFileGenerators().iterator().next(), analysis1);
+        Optional<Study> studyFromRepository1 = repository.findById(savedStudy1.getId());
+        Optional<Study> studyFromRepository2 = repository.findById(savedStudy2.getId());
+        assertTrue(studyFromRepository1.isPresent());
+        assertTrue(studyFromRepository2.isPresent());
+        assertEquals(studyFromRepository1.get().getFileGenerators().size(), 0);
+        assertEquals(studyFromRepository2.get().getFileGenerators().size(), 1);
+        assertEquals(studyFromRepository2.get().getFileGenerators().iterator().next(), analysis1);
 
         // check that just one analysis have been saved and that can be retrieved using Analysis
         // and FileGenerator repositories

variation-commons-jpa/src/test/java/uk/ac/ebi/eva/commons/jpa/models/metadata/database/StudyRelationDatabaseTest.java

@@ -98,7 +98,7 @@ public void testMultipleChildren() {
         checkChildStudiesInParent(parentStudy1, childStudies);
         checkParentStudiesInChildren(parentStudy1, childStudies);
 
-        Iterable<Study> savedChildStudies = repository.save(childStudies);
+        Iterable<Study> savedChildStudies = repository.saveAll(childStudies);
         checkChildStudiesInParent(parentStudy1, new HashSet<>((Collection<Study>) savedChildStudies));
         checkParentStudiesInChildren(parentStudy1, savedChildStudies);
 

variation-commons-mongodb/pom.xml

@@ -25,11 +25,6 @@
             <artifactId>nosqlunit-mongodb</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>com.github.fakemongo</groupId>
-            <artifactId>fongo</artifactId>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>uk.ac.ebi.eva</groupId>
             <artifactId>variation-commons-core</artifactId>

variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/configuration/EvaRepositoriesConfiguration.java

@@ -16,7 +16,6 @@
 package uk.ac.ebi.eva.commons.mongodb.configuration;
 
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.ComponentScan;

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

@@ -24,7 +24,7 @@
 /**
  * Mapped class for annotations metadata collection in mongo
  */
-@Document(collection = "#{mongoCollectionsAnnotationMetadata}")
+@Document(collection = "#{@mongoCollectionsAnnotationMetadata}")
 public class AnnotationMetadataMongo implements IAnnotationMetadata {
 
     private static final String VEP_VERSION_FIELD = "vepv";

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

@@ -31,7 +31,7 @@
 /**
  * Mapped class for annotations collection in mongo
  */
-@Document(collection = "#{mongoCollectionsAnnotations}")
+@Document(collection = "#{@mongoCollectionsAnnotations}")
 public class AnnotationMongo implements IAnnotation {
 
     public static final String CHROMOSOME_FIELD = "chr";

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

@@ -23,7 +23,7 @@
 /**
  * Mapped class for feature collection in mongo
  */
-@Document(collection = "#{mongoCollectionsFeatures}")
+@Document(collection = "#{@mongoCollectionsFeatures}")
 public class FeatureCoordinatesMongo implements IFeatureCoordinates {
 
     //TODO check if these are the intended names for the database structure

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

@@ -22,7 +22,7 @@
 
 import java.util.Set;
 
-@Document(collection = "#{mongoCollectionsSamples}")
+@Document(collection = "#{@mongoCollectionsSamples}")
 public class SampleMongo {
 
     public static final String SEX_FIELD = "sex";

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

@@ -39,7 +39,7 @@
 /**
  * Mapped class for variant collection in mongo
  */
-@Document(collection = "#{mongoCollectionsVariants}")
+@Document(collection = "#{@mongoCollectionsVariants}")
 public class VariantMongo {
 
     private static final int CHUNK_SIZE_SMALL = 1000;

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

@@ -32,7 +32,7 @@
 /**
  * Mapped class for variant source collection in mongo
  */
-@Document(collection = "#{mongoCollectionsFiles}")
+@Document(collection = "#{@mongoCollectionsFiles}")
 public class VariantSourceMongo implements IVariantSource {
 
     public final static String FILEID_FIELD = "fid";

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

@@ -15,10 +15,11 @@
  */
 package uk.ac.ebi.eva.commons.mongodb.entities.subdocuments;
 
-import com.mongodb.BasicDBObject;
+import org.bson.Document;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.data.mongodb.core.mapping.Field;
+
 import uk.ac.ebi.eva.commons.core.models.IVariantSourceEntry;
 import uk.ac.ebi.eva.commons.core.models.genotype.Genotype;
 import uk.ac.ebi.eva.commons.core.utils.CompressionHelper;
@@ -66,7 +67,7 @@ public class VariantSourceEntryMongo {
     private String[] alternates;
 
     @Field(ATTRIBUTES_FIELD)
-    private BasicDBObject attributes;
+    private Document attributes;
 
     @Field(FORMAT_FIELD)
     private String format;
@@ -115,7 +116,7 @@ public VariantSourceEntryMongo(String fileId, String studyId, String[] alternate
         }
     }
 
-    private BasicDBObject buildSampleData(List<Map<String, String>> samplesData) {
+    private Document buildSampleData(List<Map<String, String>> samplesData) {
         Map<Genotype, List<Integer>> genotypeCodes = classifySamplesByGenotype(samplesData);
 
         // Get the most common genotype
@@ -127,7 +128,7 @@ private BasicDBObject buildSampleData(List<Map<String, String>> samplesData) {
         // "def" : 0|0,
         // "0|1" : [ 41, 311, 342, 358, 881, 898, 903 ],
         // "1|0" : [ 262, 290, 300, 331, 343, 369, 374, 391, 879, 918, 930 ]
-        BasicDBObject mongoSamples = new BasicDBObject();
+        Document mongoSamples = new Document();
         if (mostCommonGenotype != null) {
             mongoSamples.append(DEFAULT, mostCommonGenotype.generateDatabaseString());
         }
@@ -172,8 +173,8 @@ private Map<Genotype, List<Integer>> classifySamplesByGenotype(List<Map<String,
         return genotypeCodes;
     }
 
-    private BasicDBObject buildAttributes(Map<String, String> attributes) {
-        BasicDBObject attrs = null;
+    private Document buildAttributes(Map<String, String> attributes) {
+        Document attrs = null;
         for (Map.Entry<String, String> entry : attributes.entrySet()) {
             Object value = entry.getValue();
             if (entry.getKey().equals("src")) {
@@ -191,7 +192,7 @@ private BasicDBObject buildAttributes(Map<String, String> attributes) {
             }
 
             if (attrs == null) {
-                attrs = new BasicDBObject(entry.getKey().replace('.', CHARACTER_TO_REPLACE_DOTS), value);
+                attrs = new Document(entry.getKey().replace('.', CHARACTER_TO_REPLACE_DOTS), value);
             } else {
                 attrs.append(entry.getKey().replace('.', CHARACTER_TO_REPLACE_DOTS), value);
             }

variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/repositories/AnnotationMetadataRepository.java

@@ -16,6 +16,7 @@
 package uk.ac.ebi.eva.commons.mongodb.repositories;
 
 import org.springframework.data.mongodb.repository.MongoRepository;
+import org.springframework.stereotype.Repository;
 
 import uk.ac.ebi.eva.commons.mongodb.entities.AnnotationMetadataMongo;
 
@@ -24,6 +25,7 @@
 /**
  * Spring MongoRepository for querying collection of AnnotationMetadataMongo documents
  */
+@Repository
 public interface AnnotationMetadataRepository extends MongoRepository<AnnotationMetadataMongo, String> {
 
     /**

variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/repositories/AnnotationRepository.java

@@ -16,6 +16,7 @@
 package uk.ac.ebi.eva.commons.mongodb.repositories;
 
 import org.springframework.data.mongodb.repository.MongoRepository;
+import org.springframework.stereotype.Repository;
 
 import uk.ac.ebi.eva.commons.core.models.IAnnotationMetadata;
 import uk.ac.ebi.eva.commons.mongodb.entities.AnnotationMongo;
@@ -31,6 +32,7 @@
 /**
  * Repository to access the annotation collection.
  */
+@Repository
 public interface AnnotationRepository extends MongoRepository<AnnotationMongo, String> {
 
     Set<AnnotationMongo> findByIdIn(Collection<String> ids);
@@ -77,14 +79,14 @@ default Map<String, AnnotationMongo> findAndIndexAnnotationsOfVariants(List<Vari
 
 
     default AnnotationMongo findOne(String chromosome, long start, String referenceAllele, String alternativeAllele,
-                                    String vepVersion, String vepCacheVersion) {
-        return findOne(AnnotationMongo.buildAnnotationId(
-                chromosome,
-                start,
-                referenceAllele,
-                alternativeAllele,
-                vepVersion,
-                vepCacheVersion));
+                                              String vepVersion, String vepCacheVersion) {
+        return findById(AnnotationMongo.buildAnnotationId(chromosome,
+                                                          start,
+                                                          referenceAllele,
+                                                          alternativeAllele,
+                                                          vepVersion,
+                                                          vepCacheVersion)).get();
+
     }
 
 }

variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/repositories/FeatureRepository.java

@@ -16,6 +16,8 @@
 package uk.ac.ebi.eva.commons.mongodb.repositories;
 
 import org.springframework.data.mongodb.repository.MongoRepository;
+import org.springframework.stereotype.Repository;
+
 import uk.ac.ebi.eva.commons.mongodb.entities.FeatureCoordinatesMongo;
 
 import java.util.List;
@@ -26,6 +28,7 @@
  * This interface is used by Spring to create the query methods for features.
  * Spring creates the implementation automatically by looking at the method name.
  */
+@Repository
 public interface FeatureRepository extends MongoRepository<FeatureCoordinatesMongo, String> {
 
     List<FeatureCoordinatesMongo> findByIdOrName(String id, String name);

variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/repositories/VariantRepository.java

@@ -21,16 +21,20 @@
 import org.springframework.data.domain.Sort;
 import org.springframework.data.mongodb.repository.MongoRepository;
 import org.springframework.data.mongodb.repository.Query;
+import org.springframework.stereotype.Repository;
+
 import uk.ac.ebi.eva.commons.core.models.VariantType;
 import uk.ac.ebi.eva.commons.mongodb.entities.VariantMongo;
 
 import java.util.List;
+import java.util.stream.Stream;
 
 /**
  * Spring MongoRepository for {@link VariantMongo} class.
  * <p>
  * Methods include querying by id, and by region.
  */
+@Repository
 public interface VariantRepository extends MongoRepository<VariantMongo, String>,
         VariantRepositoryCustom {
 
@@ -59,5 +63,9 @@ List<VariantMongo> findByChromosomeAndStartAndTypeAndStudyIn(String chr, long st
                                                                  List<String> studyIds);
 
     @Query(value = "{'chr': ?0, 'files.sid': {$in : ?1}}}")
-    VariantMongo findOneByChromosomeAndStudyInSorted(String chr, List<String> studyIds, Sort sort);
+    Stream<VariantMongo> findAllByChromosomeAndStudyInSorted(String chr, List<String> studyIds, Sort sort);
+
+    default VariantMongo findOneByChromosomeAndStudyInSorted(String chr, List<String> studyIds, Sort sort) {
+         return findAllByChromosomeAndStudyInSorted(chr, studyIds, sort).findFirst().orElse(null);
+    }
 }