IMeshService implemented

rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java

 package lcsb.mapviewer.api.mesh;
 
 import java.util.Map;
+import java.util.TreeMap;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.*;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
 
+import lcsb.mapviewer.annotation.data.MeSH;
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.services.ObjectNotFoundException;
+import lcsb.mapviewer.services.interfaces.IMeshService;
 
 @RestController
 @RequestMapping(value = "/api/mesh", produces = MediaType.APPLICATION_JSON_VALUE)
@@ -21,16 +29,26 @@ public class MeshController extends BaseController {
   @SuppressWarnings("unused")
   private Logger logger = LogManager.getLogger();
 
-  private MeshRestImpl meshRest;
+  private IMeshService meshService;
 
   @Autowired
-  public MeshController(MeshRestImpl meshRest) {
-    this.meshRest = meshRest;
+  public MeshController(IMeshService meshService) {
+    this.meshService = meshService;
   }
 
   @GetMapping(value = "/{id:.+}")
   public Map<String, Object> getMesh(@PathVariable(value = "id") String id)
       throws AnnotatorException, ObjectNotFoundException {
-    return meshRest.getMesh(id);
+
+    MeSH mesh = meshService.getMesh(new MiriamData(MiriamType.MESH_2012, id));
+    if (mesh == null) {
+      throw new ObjectNotFoundException("Object not found: " + id);
+    }
+    Map<String, Object> result = new TreeMap<>();
+    result.put("name", mesh.getName());
+    result.put("id", mesh.getMeSHId());
+    result.put("description", mesh.getDescription());
+    result.put("synonyms", mesh.getSynonyms());
+    return result;
   }
 }
\ No newline at end of file

rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java

@@ -4,13 +4,11 @@ import org.junit.runner.RunWith;
 import org.junit.runners.Suite;
 import org.junit.runners.Suite.SuiteClasses;
 
-import lcsb.mapviewer.api.mesh.AllMeshTests;
 import lcsb.mapviewer.api.projects.AllProjectTests;
 import lcsb.mapviewer.api.users.AllUserTests;
 
 @RunWith(Suite.class)
 @SuiteClasses({
-    AllMeshTests.class,
     AllProjectTests.class,
     AllUserTests.class,
 })

rest-api/src/test/java/lcsb/mapviewer/api/mesh/AllMeshTests.java

-package lcsb.mapviewer.api.mesh;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ MeshRestImplTest.class })
-public class AllMeshTests {
-
-}

rest-api/src/test/java/lcsb/mapviewer/api/mesh/MeshRestImplTest.java

-package lcsb.mapviewer.api.mesh;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.Map;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.api.RestTestFunctions;
-import lcsb.mapviewer.services.ObjectNotFoundException;
-
-public class MeshRestImplTest extends RestTestFunctions {
-
-  Logger logger = LogManager.getLogger();
-  @Autowired
-  MeshRestImpl meshRestImpl;
-
-  @Test
-  public void test() throws ObjectNotFoundException, AnnotatorException {
-    Map<String, Object> result = meshRestImpl.getMesh("D010300");
-    assertNotNull(result);
-    String name = (String) result.get("name");
-    assertTrue(name.toLowerCase().contains("parkinson"));
-  }
-
-}

rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshRestImpl.java → service/src/main/java/lcsb/mapviewer/services/impl/MeshService.java

-package lcsb.mapviewer.api.mesh;
+package lcsb.mapviewer.services.impl;
 
-import java.util.Map;
-import java.util.TreeMap;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
@@ -12,39 +7,23 @@ import org.springframework.transaction.annotation.Transactional;
 import lcsb.mapviewer.annotation.data.MeSH;
 import lcsb.mapviewer.annotation.services.MeSHParser;
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.api.BaseRestImpl;
 import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.services.ObjectNotFoundException;
+import lcsb.mapviewer.services.interfaces.IMeshService;
 
 @Transactional
 @Service
-public class MeshRestImpl extends BaseRestImpl {
-
-  /**
-   * Default class logger.
-   */
-  @SuppressWarnings("unused")
-  private Logger logger = LogManager.getLogger();
+public class MeshService implements IMeshService {
 
   private MeSHParser meSHParser;
 
   @Autowired
-  public MeshRestImpl(MeSHParser meSHParser) {
+  public MeshService(MeSHParser meSHParser) {
     this.meSHParser = meSHParser;
   }
 
-  public Map<String, Object> getMesh(String id) throws AnnotatorException, ObjectNotFoundException {
 
-    MeSH mesh = meSHParser.getMeSH(new MiriamData(MiriamType.MESH_2012, id));
-    if (mesh == null) {
-      throw new ObjectNotFoundException("Object not found: " + id);
-    }
-    Map<String, Object> result = new TreeMap<>();
-    result.put("name", mesh.getName());
-    result.put("id", mesh.getMeSHId());
-    result.put("description", mesh.getDescription());
-    result.put("synonyms", mesh.getSynonyms());
-    return result;
+  @Override
+  public MeSH getMesh(MiriamData meshID) throws AnnotatorException {
+    return meSHParser.getMeSH(meshID);
   }
 }

service/src/main/java/lcsb/mapviewer/services/interfaces/IMeshService.java

+package lcsb.mapviewer.services.interfaces;
+
+import lcsb.mapviewer.annotation.data.MeSH;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.model.map.MiriamData;
+
+public interface IMeshService {
+
+  MeSH getMesh(MiriamData miriamData) throws AnnotatorException;
+}

web/src/test/java/lcsb/mapviewer/web/MeshControllerIntegrationTest.java

 package lcsb.mapviewer.web;
 
+import static org.junit.Assert.assertTrue;
 import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.document;
 import static org.springframework.restdocs.mockmvc.RestDocumentationRequestBuilders.get;
 import static org.springframework.restdocs.payload.PayloadDocumentation.fieldWithPath;
@@ -8,18 +9,29 @@ import static org.springframework.restdocs.request.RequestDocumentation.paramete
 import static org.springframework.restdocs.request.RequestDocumentation.pathParameters;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
 
+import java.util.Map;
+
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.junit.*;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
 import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.test.web.servlet.RequestBuilder;
 
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
 @RunWith(SpringJUnit4ClassRunner.class)
 public class MeshControllerIntegrationTest extends ControllerIntegrationTest {
 
   Logger logger = LogManager.getLogger();
 
+  @Autowired
+  private ObjectMapper objectMapper;
+
   @Before
   public void setup() {
   }
@@ -31,9 +43,9 @@ public class MeshControllerIntegrationTest extends ControllerIntegrationTest {
   @Test
   public void testGetTaxonomies() throws Exception {
 
-    RequestBuilder request = get("/api/mesh/{meshId}", "D002095");
+    RequestBuilder request = get("/api/mesh/{meshId}", "D010300");
 
-    mockMvc.perform(request)
+    String response = mockMvc.perform(request)
         .andDo(document("mesh/get_mesh",
             pathParameters(parameterWithName("meshId").description("mesh id")),
             responseFields(
@@ -49,7 +61,14 @@ public class MeshControllerIntegrationTest extends ControllerIntegrationTest {
                 fieldWithPath("id")
                     .description("mesh id")
                     .type("string"))))
-        .andExpect(status().is2xxSuccessful());
+        .andExpect(status().is2xxSuccessful())
+        .andReturn().getResponse().getContentAsString();
+
+    Map<String, Object> result = objectMapper.readValue(response, new TypeReference<Map<String, Object>>() {
+    });
+    String name = (String) result.get("name");
+    assertTrue(name.toLowerCase().contains("parkinson"));
+
   }
 
 }