EVA-1063 - Add supporting entity, service and repository to support default locus range service

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

@@ -0,0 +1,87 @@
+/*
+ * Copyright 2019 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package uk.ac.ebi.eva.commons.core.models;
+
+/**
+ * Base implementation of {@link IDefaultLocusRangeMetadata}
+ */
+public class DefaultLocusRangeMetadata implements IDefaultLocusRangeMetadata {
+
+    private String chromosome;
+
+    private long start;
+
+    private long end;
+
+    public DefaultLocusRangeMetadata() {
+
+    }
+
+    public DefaultLocusRangeMetadata(IDefaultLocusRangeMetadata defaultLocusRangeMetadata) {
+        this(defaultLocusRangeMetadata.getChromosome(), defaultLocusRangeMetadata.getStart(),
+                defaultLocusRangeMetadata.getEnd());
+    }
+
+    public DefaultLocusRangeMetadata(String chromosome, long start, long end) {
+        this.chromosome = chromosome;
+        this.start = start;
+        this.end = end;
+    }
+
+    @Override
+    public String getChromosome() {
+        return chromosome;
+    }
+
+    @Override
+    public long getStart() {
+        return start;
+    }
+
+    @Override
+    public long getEnd() {
+        return end;
+    }
+
+    @Override
+    public String toString() {
+        return "DefaultLocusRangeMetadata{" +
+                "chromosome='" + chromosome + '\'' +
+                ", start='" + start + '\'' +
+                ", end='" + end + '\'' +
+                '}';
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+
+        DefaultLocusRangeMetadata that = (DefaultLocusRangeMetadata) o;
+
+        if (start != that.start) return false;
+        if (end != that.end) return false;
+        return chromosome.equals(that.chromosome);
+    }
+
+    @Override
+    public int hashCode() {
+        int result = chromosome.hashCode();
+        result = 31 * result + (int) (start ^ (start >>> 32));
+        result = 31 * result + (int) (end ^ (end >>> 32));
+        return result;
+    }
+}

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

@@ -0,0 +1,26 @@
+/*
+ * Copyright 2019 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package uk.ac.ebi.eva.commons.core.models;
+
+public interface IDefaultLocusRangeMetadata {
+
+    String getChromosome();
+
+    long getStart();
+
+    long getEnd();
+
+}

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

@@ -0,0 +1,108 @@
+/*
+ * Copyright 2019 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package uk.ac.ebi.eva.commons.mongodb.entities;
+
+import org.springframework.data.annotation.Id;
+import org.springframework.data.mongodb.core.mapping.Document;
+import org.springframework.data.mongodb.core.mapping.Field;
+import uk.ac.ebi.eva.commons.core.models.IDefaultLocusRangeMetadata;
+
+/**
+ * Mapped class for annotations metadata collection in mongo
+ */
+@Document(collection = "#{mongoCollectionsDefaultLocusRangeMetadata}")
+public class DefaultLocusRangeMetadataMongo implements IDefaultLocusRangeMetadata {
+
+    private static final String CHROMOSOME_FIELD = "chr";
+
+    private static final String START_FIELD = "start";
+
+    private static final String END_FIELD = "end";
+
+    @Id
+    private String id;
+
+    @Field(CHROMOSOME_FIELD)
+    private String chromosome;
+
+    @Field(START_FIELD)
+    private long start;
+
+    @Field(END_FIELD)
+    private long end;
+
+    DefaultLocusRangeMetadataMongo() {
+        // Empty document constructor for spring-data
+    }
+
+    public DefaultLocusRangeMetadataMongo(String id, String chromosome, long start, long end) {
+        this.id = id;
+        this.chromosome = chromosome;
+        this.start = start;
+        this.end = end;
+    }
+
+    public String getId() {
+        return id;
+    }
+
+    public void setId(String id) {
+        this.id = id;
+    }
+
+    public String getChromosome() {
+        return chromosome;
+    }
+
+    public long getStart() {
+        return start;
+    }
+
+    public long getEnd() {
+        return end;
+    }
+
+    @Override
+    public String toString() {
+        return "DefaultLocusRangeMetadataMongo{" +
+                "chromosome='" + chromosome + '\'' +
+                ", start='" + start + '\'' +
+                ", end='" + end + '\'' +
+                '}';
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+
+        DefaultLocusRangeMetadataMongo that = (DefaultLocusRangeMetadataMongo) o;
+
+        if (id != null ? !id.equals(that.id) : that.id != null) return false;
+        if (start != that.start) return false;
+        if (end != that.end) return false;
+        return chromosome.equals(that.chromosome);
+    }
+
+    @Override
+    public int hashCode() {
+        int result = id != null ? id.hashCode() : 0;
+        result = 31 * result + (chromosome != null ? chromosome.hashCode() : 0);
+        result = 31 * result + (int) (start ^ (start >>> 32));
+        result = 31 * result + (int) (end ^ (end >>> 32));
+        return result;
+    }
+}

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

@@ -0,0 +1,34 @@
+/*
+ * Copyright 2019 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package uk.ac.ebi.eva.commons.mongodb.repositories;
+
+import org.springframework.data.mongodb.repository.MongoRepository;
+import uk.ac.ebi.eva.commons.mongodb.entities.DefaultLocusRangeMetadataMongo;
+
+import java.util.List;
+
+/**
+ * Spring MongoRepository for querying collection of DefaultLocusRangeMetadataMongo documents
+ */
+public interface DefaultLocusRangeMetadataRepository extends MongoRepository<DefaultLocusRangeMetadataMongo, String> {
+
+    /**
+     * Query for all DefaultLocusRangeMetadataMongo from collection
+     *
+     * @return List of DefaultLocusRangeMetadataMongo objects
+     */
+    List<DefaultLocusRangeMetadataMongo> findAllByOrderByChromosomeAscStartAscEndAsc();
+}

variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/services/DefaultLocusRangeMetadataService.java

@@ -0,0 +1,44 @@
+/*
+ * Copyright 2019 EMBL - European Bioinformatics Institute
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package uk.ac.ebi.eva.commons.mongodb.services;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import uk.ac.ebi.eva.commons.core.models.DefaultLocusRangeMetadata;
+import uk.ac.ebi.eva.commons.mongodb.entities.DefaultLocusRangeMetadataMongo;
+import uk.ac.ebi.eva.commons.mongodb.repositories.DefaultLocusRangeMetadataRepository;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+/**
+ * Mongo persistence service to access {@link DefaultLocusRangeMetadata}
+ */
+@Service
+public class DefaultLocusRangeMetadataService {
+
+    @Autowired
+    private DefaultLocusRangeMetadataRepository repository;
+
+    public List<DefaultLocusRangeMetadata> findAllByOrderByChromosomeAscStartAscEndAsc() {
+        return convert(repository.findAllByOrderByChromosomeAscStartAscEndAsc());
+    }
+
+    private List<DefaultLocusRangeMetadata> convert(List<DefaultLocusRangeMetadataMongo> defaultLocusRangeMetadatas) {
+        return defaultLocusRangeMetadatas.stream().map(DefaultLocusRangeMetadata::new).collect(Collectors.toList());
+    }
+
+}

variation-commons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/DatabaseTestConfiguration.java

@@ -29,9 +29,17 @@ public class DatabaseTestConfiguration {
     @Value("${db.collections.annotation-metadata.name}")
     public String mongoCollectionsAnnotationMetadata;
 
+    @Value("${db.collections.default-locus-range-metadata.name}")
+    public String mongoCollectionsDefaultLocusRangeMetadata;
+
     @Bean
     public String mongoCollectionsAnnotationMetadata() {
         return mongoCollectionsAnnotationMetadata;
     }
 
+    @Bean
+    public String mongoCollectionsDefaultLocusRangeMetadata() {
+        return mongoCollectionsDefaultLocusRangeMetadata;
+    }
+
 }

variation-commons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/configuration/MongoRepositoryTestConfiguration.java

@@ -44,6 +44,14 @@ public String mongoCollectionsAnnotationMetadata(
         return collectionAnnotationMetadata;
     }
 
+    @Bean
+    public String mongoCollectionsDefaultLocusRangeMetadata(
+            @Value("${eva.mongo.collections.default-locus-range-metadata:#{null}}")
+                    String collectionDefaultLocusRangeMetadata) {
+        Assert.notNull(collectionDefaultLocusRangeMetadata);
+        return collectionDefaultLocusRangeMetadata;
+    }
+
     @Bean
     public String mongoCollectionsAnnotations(
             @Value("${eva.mongo.collections.annotations:#{null}}") String collectionAnnotations) {

variation-commons-mongodb/src/test/java/uk/ac/ebi/eva/commons/mongodb/repositories/DefaultLocusRangeMetadataRepositoryTest.java

@@ -0,0 +1,41 @@
+package uk.ac.ebi.eva.commons.mongodb.repositories;
+
+import com.lordofthejars.nosqlunit.annotation.UsingDataSet;
+import com.lordofthejars.nosqlunit.mongodb.MongoDbRule;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.ApplicationContext;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+
+import uk.ac.ebi.eva.commons.mongodb.configuration.MongoRepositoryTestConfiguration;
+import uk.ac.ebi.eva.commons.mongodb.entities.DefaultLocusRangeMetadataMongo;
+
+import java.util.List;
+
+import static com.lordofthejars.nosqlunit.mongodb.MongoDbRule.MongoDbRuleBuilder.newMongoDbRule;
+import static org.junit.Assert.*;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+@ContextConfiguration(classes = {MongoRepositoryTestConfiguration.class})
+@UsingDataSet(locations = {"/test-data/defaultLocusRange.json"})
+public class DefaultLocusRangeMetadataRepositoryTest {
+
+    @Autowired
+    private ApplicationContext applicationContext;
+
+    @Rule
+    public MongoDbRule mongoDbRule = newMongoDbRule().defaultSpringMongoDb("test-db");
+
+    @Autowired
+    private DefaultLocusRangeMetadataRepository repository;
+
+    @Test
+    public void findOneByDefault() throws Exception {
+        List<DefaultLocusRangeMetadataMongo> defaultLocusRangeMetadataMongoList =
+                repository.findAllByOrderByChromosomeAscStartAscEndAsc();
+        assertEquals(1, defaultLocusRangeMetadataMongoList.size());
+    }
+}