EVA-1063 - Add service end point to provide default locus range for a given species

eva-lib/src/main/java/uk/ac/ebi/eva/lib/MongoConfiguration.java

@@ -62,6 +62,11 @@ public String mongoCollectionsAnnotationMetadata() {
         return dbCollectionsProperties.getAnnotationMetadata();
     }
 
+    @Bean
+    public String mongoCollectionsDefaultLocusRangeMetadata() {
+        return dbCollectionsProperties.getDefaultLocusRangeMetadata();
+    }
+
     @Bean
     public String mongoCollectionsAnnotations() {
         return dbCollectionsProperties.getAnnotations();

eva-lib/src/main/java/uk/ac/ebi/eva/lib/configuration/DbCollectionsProperties.java

@@ -39,6 +39,10 @@ public class DbCollectionsProperties {
     @NotNull
     private String annotationMetadata;
 
+    @Size(min = 1)
+    @NotNull
+    private String defaultLocusRangeMetadata;
+
     @Size(min = 1)
     @NotNull
     private String annotations;
@@ -67,10 +71,18 @@ public String getAnnotationMetadata() {
         return annotationMetadata;
     }
 
+    public String getDefaultLocusRangeMetadata() {
+        return defaultLocusRangeMetadata;
+    }
+
     public void setAnnotationMetadata(String annotationMetadata) {
         this.annotationMetadata = annotationMetadata;
     }
 
+    public void setDefaultLocusRangeMetadata(String defaultLocusRangeMetadata) {
+        this.defaultLocusRangeMetadata = defaultLocusRangeMetadata;
+    }
+
     public String getAnnotations() {
         return annotations;
     }

eva-server/src/main/java/uk/ac/ebi/eva/server/ws/DefaultLocusRangeMetadataWSServer.java

@@ -0,0 +1,55 @@
+/*
+ * 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.server.ws;
+
+import io.swagger.annotations.Api;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.web.bind.annotation.*;
+import uk.ac.ebi.eva.commons.core.models.DefaultLocusRangeMetadata;
+import uk.ac.ebi.eva.commons.mongodb.services.DefaultLocusRangeMetadataService;
+import uk.ac.ebi.eva.lib.eva_utils.DBAdaptorConnector;
+import uk.ac.ebi.eva.lib.eva_utils.MultiMongoDbFactory;
+import uk.ac.ebi.eva.lib.utils.QueryResponse;
+import uk.ac.ebi.eva.lib.utils.QueryResult;
+
+import javax.servlet.http.HttpServletResponse;
+import java.util.List;
+
+@RestController
+@RequestMapping(value = "/v1/default-locus-range", produces = "application/json")
+@Api(tags = {"default-locus-range"})
+public class DefaultLocusRangeMetadataWSServer extends EvaWSServer {
+
+    @Autowired
+    private DefaultLocusRangeMetadataService service;
+
+    @RequestMapping(value = "", method = RequestMethod.GET)
+    @ResponseBody
+    public QueryResponse getDefaultLocusRangeMetadata(@RequestParam(name = "species") String species,
+                                               HttpServletResponse response) {
+        if (species.isEmpty()) {
+            response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
+            return setQueryResponse("Please specify a species");
+        }
+
+        MultiMongoDbFactory.setDatabaseNameForCurrentThread(DBAdaptorConnector.getDBName(species));
+        List<DefaultLocusRangeMetadata> defaultLocusRangeMetadataList =
+                service.findAllByOrderByChromosomeAscStartAscEndAsc();
+        QueryResult<DefaultLocusRangeMetadata> queryResult = buildQueryResult(defaultLocusRangeMetadataList);
+        return setQueryResponse(queryResult);
+    }
+
+}

eva-server/src/test/java/uk/ac/ebi/eva/server/ws/DefaultLocusRangeMetadataWSServerTest.java

@@ -0,0 +1,81 @@
+/*
+ * 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.server.ws;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.boot.test.web.client.TestRestTemplate;
+import org.springframework.core.ParameterizedTypeReference;
+import org.springframework.http.HttpMethod;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.test.context.junit4.SpringRunner;
+import uk.ac.ebi.eva.commons.core.models.DefaultLocusRangeMetadata;
+import uk.ac.ebi.eva.commons.mongodb.services.DefaultLocusRangeMetadataService;
+import uk.ac.ebi.eva.lib.utils.QueryResponse;
+import uk.ac.ebi.eva.lib.utils.QueryResult;
+
+import java.util.Arrays;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.mockito.BDDMockito.given;
+
+@RunWith(SpringRunner.class)
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
+public class DefaultLocusRangeMetadataWSServerTest {
+
+    private List<DefaultLocusRangeMetadata> defaultLocusRangeMetadataList;
+
+    @Autowired
+    private TestRestTemplate restTemplate;
+
+    @MockBean
+    private DefaultLocusRangeMetadataService service;
+
+    @Before
+    public void setUp() throws Exception {
+        defaultLocusRangeMetadataList = Arrays.asList(new DefaultLocusRangeMetadata("1", 1, 1000000));
+
+        given(service.findAllByOrderByChromosomeAscStartAscEndAsc()).willReturn(defaultLocusRangeMetadataList);
+    }
+
+    @Test
+    public void testDefaultLocusRangeMetadata() {
+        String url = "/v1/default-locus-range?species=mmusculus_grcm38";
+        ResponseEntity<QueryResponse<QueryResult<DefaultLocusRangeMetadata>>> response = restTemplate.exchange(
+                url, HttpMethod.GET, null,
+                new ParameterizedTypeReference<QueryResponse<QueryResult<DefaultLocusRangeMetadata>>>() {
+                });
+        assertEquals(HttpStatus.OK, response.getStatusCode());
+
+        QueryResponse<QueryResult<DefaultLocusRangeMetadata>> queryResponse = response.getBody();
+        assertEquals(1, queryResponse.getResponse().size());
+
+        List<DefaultLocusRangeMetadata> results = queryResponse.getResponse().get(0).getResult();
+        assertEquals(defaultLocusRangeMetadataList.size(), results.size());
+
+        for (DefaultLocusRangeMetadata result : results) {
+            assertTrue(defaultLocusRangeMetadataList.contains(result));
+        }
+    }
+
+}

eva-server/src/test/resources/application.properties

@@ -7,5 +7,6 @@ spring.data.mongodb.read-preference=
 db.collection-names.files=testFiles
 db.collection-names.variants=testVariants
 db.collection-names.annotation-metadata=testMetadata
+db.collection-names.default-locus-range-metadata=testDefaultLocusRange
 db.collection-names.annotations=testAnnotations
 db.collection-names.features=testFeatures