Study ws server v2

eva-server/src/main/java/uk/ac/ebi/eva/server/ws/StudyWSServerV2.java

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+package uk.ac.ebi.eva.server.ws;
+
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiParam;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.hateoas.Link;
+import org.springframework.hateoas.PagedResources;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+import uk.ac.ebi.eva.commons.mongodb.entities.projections.VariantStudySummary;
+import uk.ac.ebi.eva.commons.mongodb.services.VariantStudySummaryService;
+import uk.ac.ebi.eva.lib.eva_utils.DBAdaptorConnector;
+import uk.ac.ebi.eva.lib.eva_utils.MultiMongoDbFactory;
+
+import java.util.Collections;
+import java.util.List;
+
+import static org.springframework.hateoas.mvc.ControllerLinkBuilder.linkTo;
+import static org.springframework.hateoas.mvc.ControllerLinkBuilder.methodOn;
+
+@RestController
+@RequestMapping(value = "/v2/studies", produces = "application/hal+json")
+@Api(tags = "studies")
+public class StudyWSServerV2 {
+
+    @Autowired
+    private VariantStudySummaryService variantStudySummaryService;
+
+    @RequestMapping(value = "", method = RequestMethod.GET)
+    public ResponseEntity getBrowsableStudies(
+            @ApiParam(value = "First letter of the genus, followed by the full species name, e.g. hsapiens. " +
+                    "Allowed values can be looked up in /v1/meta/species/list/ in the field named" +
+                    " 'taxonomyCode'.", required = true)
+            @RequestParam("species") String species,
+            @ApiParam(value = "Encoded assembly name, e.g. grch37. Allowed values can be looked up in " +
+                    "/v1/meta/species/list/ in the field named 'assemblyCode'.", required = true)
+            @RequestParam("assembly") String assembly,
+            @ApiParam(value = "The number of the page that should be displayed. Starts from 0 and is an integer." +
+                    " e.g. 0")
+            @RequestParam(required = false, defaultValue = "0") Integer pageNumber,
+            @ApiParam(value = "The number of elements that should be displayed in a single page. e.g. 5")
+            @RequestParam(required = false, defaultValue = "20") Integer pageSize)
+            throws IllegalArgumentException {
+        if (species == null || species.isEmpty()) {
+            throw new IllegalArgumentException("Please specify a species");
+        }
+
+        MultiMongoDbFactory.setDatabaseNameForCurrentThread(DBAdaptorConnector.getDBName(species + "_" + assembly));
+
+        int totalNumberOfResults = variantStudySummaryService.countAll();
+        if (totalNumberOfResults == 0) {
+            return new ResponseEntity(new PagedResources<>(Collections.EMPTY_LIST, new PagedResources.PageMetadata
+                    (pageSize, pageNumber < 0 ? 0 : pageNumber, totalNumberOfResults)), HttpStatus.NO_CONTENT);
+        }
+
+        List<VariantStudySummary> uniqueStudies = variantStudySummaryService.findAll(pageNumber, pageSize);
+
+        PagedResources.PageMetadata pageMetadata;
+        try {
+            pageMetadata = buildPageMetadata(pageSize, pageNumber, totalNumberOfResults);
+        } catch (IllegalArgumentException e) {
+            return new ResponseEntity(e.getMessage(), HttpStatus.REQUESTED_RANGE_NOT_SATISFIABLE);
+        }
+
+        PagedResources pagedResources = buildPagedResources(uniqueStudies, species, assembly, pageMetadata);
+        return new ResponseEntity(pagedResources, HttpStatus.OK);
+    }
+
+    private PagedResources.PageMetadata buildPageMetadata(Integer pageSize, Integer pageNumber, Integer
+            totalNumberOfResults)
+            throws IllegalArgumentException {
+        Long totalPages = pageSize == 0L ? 0L : (long) Math.ceil((double) totalNumberOfResults / (double) pageSize);
+
+        if (pageNumber < 0 || pageNumber >= totalPages) {
+            throw new IllegalArgumentException("For the given page size, there are " + totalPages + " page(s), so " +
+                    "the correct page range is from 0 to " + (totalPages - 1) + " (both included).");
+        }
+        return new PagedResources.PageMetadata(pageSize, pageNumber, totalNumberOfResults, totalPages);
+    }
+
+    private PagedResources buildPagedResources(List<VariantStudySummary> uniqueStudies, String species,
+                                               String assembly, PagedResources.PageMetadata pageMetadata) {
+
+        PagedResources pagedResources = new PagedResources<>(uniqueStudies, pageMetadata);
+
+        int pageNumber = (int) pageMetadata.getNumber();
+        int pageSize = (int) pageMetadata.getSize();
+
+        if (pageNumber > 0) {
+            pagedResources.add(createPaginationLink(species, assembly, pageNumber - 1, pageSize, "prev"));
+
+            pagedResources.add(createPaginationLink(species, assembly, 0, pageSize, "first"));
+        }
+
+        if (pageNumber < (pageMetadata.getTotalPages() - 1)) {
+            pagedResources.add(createPaginationLink(species, assembly, pageNumber + 1, pageSize, "next"));
+
+            pagedResources.add(createPaginationLink(species, assembly, (int) pageMetadata.getTotalPages() - 1,
+                    pageSize, "last"));
+        }
+        return pagedResources;
+    }
+
+    private Link createPaginationLink(String species, String assembly, int pageNumber, int pageSize, String linkName) {
+        return new Link(linkTo(methodOn(StudyWSServerV2.class).getBrowsableStudies(species, assembly,
+                pageNumber, pageSize))
+                .toUriComponentsBuilder()
+                .toUriString(), linkName);
+    }
+}

eva-server/src/test/java/uk/ac/ebi/eva/server/ws/StudyWSServerV2IntegrationTest.java

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+/*
+ * European Variation Archive (EVA) - Open-access database of all types of genetic
+ * variation data from all species
+ *
+ * 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 com.fasterxml.jackson.databind.ObjectMapper;
+import com.jayway.jsonpath.Configuration;
+import com.jayway.jsonpath.JsonPath;
+import com.jayway.jsonpath.Option;
+import com.jayway.jsonpath.TypeRef;
+import com.jayway.jsonpath.spi.json.JacksonJsonProvider;
+import com.jayway.jsonpath.spi.mapper.JacksonMappingProvider;
+import com.lordofthejars.nosqlunit.annotation.UsingDataSet;
+import com.lordofthejars.nosqlunit.mongodb.MongoDbRule;
+import org.junit.Before;
+import org.junit.Rule;
+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.web.client.TestRestTemplate;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.annotation.Import;
+import org.springframework.data.mongodb.MongoDbFactory;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.test.context.ActiveProfiles;
+import org.springframework.test.context.junit4.SpringRunner;
+
+import uk.ac.ebi.eva.commons.core.models.pipeline.Variant;
+import uk.ac.ebi.eva.commons.mongodb.entities.projections.VariantStudySummary;
+import uk.ac.ebi.eva.commons.mongodb.services.VariantWithSamplesAndAnnotationsService;
+import uk.ac.ebi.eva.lib.Profiles;
+import uk.ac.ebi.eva.server.configuration.MongoRepositoryTestConfiguration;
+
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.List;
+
+import static com.lordofthejars.nosqlunit.mongodb.MongoDbRule.MongoDbRuleBuilder.newMongoDbRule;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+
+@RunWith(SpringRunner.class)
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
+@Import({MongoRepositoryTestConfiguration.class})
+@UsingDataSet(locations = {
+        "/test-data/files.json"
+})
+@ActiveProfiles(Profiles.TEST_MONGO_FACTORY)
+public class StudyWSServerV2IntegrationTest {
+
+    private static final String TEST_DB = "test-db";
+
+    @Autowired
+    private ApplicationContext applicationContext;
+
+    @Rule
+    public MongoDbRule mongoDbRule = newMongoDbRule().defaultSpringMongoDb(TEST_DB);
+
+    @Autowired
+    MongoDbFactory mongoDbFactory;
+
+    @Autowired
+    private TestRestTemplate restTemplate;
+
+    @Autowired
+    private ObjectMapper objectMapper;
+
+    @Test
+    public void testGetStudies() {
+        String url = "/v2/studies?species=mmusculus&assembly=grcm38&pageNumber=0&pageSize=1";
+        ResponseEntity<String> response = restTemplate.getForEntity(url, String.class);
+        assertEquals(HttpStatus.OK, response.getStatusCode());
+
+        Configuration configuration = Configuration.defaultConfiguration()
+                .jsonProvider(new JacksonJsonProvider())
+                .mappingProvider(new JacksonMappingProvider(objectMapper))
+                .addOptions(Option.SUPPRESS_EXCEPTIONS);
+
+        List<VariantStudySummary> variantList = JsonPath.using(configuration).parse(response.getBody())
+                .read("$['_embedded']['variantStudySummaryList']", new TypeRef<List<VariantStudySummary>>() {
+                });
+
+        assertEquals("PRJX00001", variantList.get(0).getStudyId());
+        assertEquals("Human Variation Data From dbSNP build 144", variantList.get(0).getStudyName());
+        assertEquals(1, variantList.size());
+
+        Integer totalNumberOfElements = JsonPath.using(configuration).parse(response.getBody())
+                .read("$['page']['totalElements']", Integer.class);
+        Integer pageNumber = JsonPath.using(configuration).parse(response.getBody())
+                .read("$['page']['number']", Integer.class);
+        Integer size = JsonPath.using(configuration).parse(response.getBody())
+                .read("$['page']['size']", Integer.class);
+        Integer totalPages = JsonPath.using(configuration).parse(response.getBody())
+                .read("$['page']['totalPages']", Integer.class);
+
+        assertEquals(2, totalNumberOfElements.intValue());
+        assertEquals(0, pageNumber.intValue());
+        assertEquals(1, size.intValue());
+        assertEquals(2, totalPages.intValue());
+    }
+
+    @Test
+    public void testInvalidPageRanges() {
+        String url = "/v2/studies?species=mmusculus&assembly=grcm38&pageNumber=1000&pageSize=1";
+        ResponseEntity<String> response = restTemplate.getForEntity(url, String.class);
+        assertEquals(HttpStatus.REQUESTED_RANGE_NOT_SATISFIABLE, response.getStatusCode());
+        assertEquals("For the given page size, there are 2 page(s), so the correct page range is from 0 to 1" +
+                " (both included).", response.getBody());
+    }
+}

eva-server/src/test/java/uk/ac/ebi/eva/server/ws/StudyWSServerV2Test.java

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+package uk.ac.ebi.eva.server.ws;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.jayway.jsonpath.Configuration;
+import com.jayway.jsonpath.JsonPath;
+import com.jayway.jsonpath.Option;
+import com.jayway.jsonpath.TypeRef;
+import com.jayway.jsonpath.spi.json.JacksonJsonProvider;
+import com.jayway.jsonpath.spi.mapper.JacksonMappingProvider;
+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.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.test.context.junit4.SpringRunner;
+import uk.ac.ebi.eva.commons.mongodb.entities.projections.VariantStudySummary;
+import uk.ac.ebi.eva.commons.mongodb.services.VariantStudySummaryService;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static org.mockito.BDDMockito.given;
+import static org.mockito.Matchers.eq;
+
+@RunWith(SpringRunner.class)
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
+public class StudyWSServerV2Test {
+
+    private static final long PAGE_SIZE = 2;
+
+    private static final long PAGE_NUMBER = 0;
+
+    @Autowired
+    private TestRestTemplate restTemplate;
+
+    @MockBean
+    private VariantStudySummaryService service;
+
+    @Autowired
+    private ObjectMapper objectMapper;
+
+    @Before
+    public void setUp() {
+        List<VariantStudySummary> studies = new ArrayList<>();
+        VariantStudySummary study1 = new VariantStudySummary();
+        VariantStudySummary study2 = new VariantStudySummary();
+
+        study1.setFilesCount(1);
+        study1.setStudyId("studyId1");
+        study1.setStudyName("studyName1");
+        studies.add(study1);
+
+        study2.setFilesCount(2);
+        study2.setStudyId("studyId2");
+        study2.setStudyName("studyName2");
+        studies.add(study2);
+
+        given(service.findAll(eq(PAGE_NUMBER), eq(PAGE_SIZE))).willReturn(studies);
+        given(service.countAll()).willReturn(2);
+    }
+
+    @Test
+    public void testGetStudies() {
+        String url = "/v2/studies?species=mmusculus&assembly=grcm38&pageNumber=0&pageSize=2";
+        ResponseEntity<String> response = restTemplate.getForEntity(url, String.class);
+        assertEquals(HttpStatus.OK, response.getStatusCode());
+
+        Configuration configuration = Configuration.defaultConfiguration()
+                .jsonProvider(new JacksonJsonProvider())
+                .mappingProvider(new JacksonMappingProvider(objectMapper))
+                .addOptions(Option.SUPPRESS_EXCEPTIONS);
+
+        List<VariantStudySummary> variantList = JsonPath.using(configuration).parse(response.getBody())
+                .read("$['_embedded']['variantStudySummaryList']", new TypeRef<List<VariantStudySummary>>() {
+                });
+        assertEquals("studyId1", variantList.get(0).getStudyId());
+        assertEquals("studyName1", variantList.get(0).getStudyName());
+        assertEquals("studyId2", variantList.get(1).getStudyId());
+        assertEquals("studyName2", variantList.get(1).getStudyName());
+    }
+}