get submodel connections moved to controller

model/src/main/java/lcsb/mapviewer/modelutils/serializer/id/ModelDataAsModelIdSerializer.java

+package lcsb.mapviewer.modelutils.serializer.id;
+
+import java.io.IOException;
+
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.databind.JsonSerializer;
+import com.fasterxml.jackson.databind.SerializerProvider;
+
+import lcsb.mapviewer.model.map.model.ModelData;
+
+public class ModelDataAsModelIdSerializer extends JsonSerializer<ModelData> {
+
+  @Override
+  public void serialize(final ModelData model, final JsonGenerator gen, final SerializerProvider serializers)
+      throws IOException {
+    gen.writeStartObject();
+    gen.writeNumberField("modelId", model.getId());
+    gen.writeEndObject();
+  }
+}
\ No newline at end of file

rest-api/src/main/java/lcsb/mapviewer/api/ElementIdentifierType.java → model/src/main/java/lcsb/mapviewer/modelutils/serializer/model/map/ElementIdentifierType.java

-package lcsb.mapviewer.api;
+package lcsb.mapviewer.modelutils.serializer.model.map;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;

model/src/main/java/lcsb/mapviewer/modelutils/serializer/model/map/MinifiedBioEntitySerializer.java

+package lcsb.mapviewer.modelutils.serializer.model.map;
+
+import java.io.IOException;
+
+import com.fasterxml.jackson.core.JsonGenerator;
+import com.fasterxml.jackson.databind.JsonSerializer;
+import com.fasterxml.jackson.databind.SerializerProvider;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+
+public class MinifiedBioEntitySerializer extends JsonSerializer<BioEntity> {
+
+  @Override
+  public void serialize(final BioEntity object, final JsonGenerator gen,
+      final SerializerProvider serializers)
+      throws IOException {
+    gen.writeStartObject();
+    gen.writeNumberField("id", object.getId());
+    gen.writeNumberField("modelId", object.getModelData().getId());
+    if (object instanceof Element) {
+      gen.writeObjectField("type", ElementIdentifierType.ALIAS);
+    } else if (object instanceof Reaction) {
+      gen.writeObjectField("type", ElementIdentifierType.REACTION);
+    } else {
+      throw new InvalidStateException("Unknown type of result: " + object.getClass());
+    }
+    gen.writeEndObject();
+  }
+}
\ No newline at end of file

rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java

@@ -44,6 +44,7 @@ import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
+import lcsb.mapviewer.modelutils.serializer.model.map.ElementIdentifierType;
 import lcsb.mapviewer.persist.dao.map.species.ElementProperty;
 import lcsb.mapviewer.services.QueryException;
 import lcsb.mapviewer.services.interfaces.IConfigurationService;

rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java

@@ -7,6 +7,7 @@ import java.lang.reflect.InvocationTargetException;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -42,6 +43,7 @@ import org.springframework.web.bind.annotation.RestController;
 import com.fasterxml.jackson.annotation.JsonCreator;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.api.BaseController;
@@ -54,11 +56,17 @@ import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.ProjectLogEntry;
 import lcsb.mapviewer.model.cache.UploadedFileEntry;
 import lcsb.mapviewer.model.graphics.MapCanvasType;
+import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.layout.ProjectBackground;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.security.PrivilegeType;
 import lcsb.mapviewer.model.user.ConfigurationElementType;
 import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.modelutils.serializer.id.ModelDataAsModelIdSerializer;
+import lcsb.mapviewer.modelutils.serializer.model.map.MinifiedBioEntitySerializer;
+import lcsb.mapviewer.persist.dao.map.species.ElementProperty;
 import lcsb.mapviewer.services.ObjectExistsException;
 import lcsb.mapviewer.services.ObjectNotFoundException;
 import lcsb.mapviewer.services.QueryException;
@@ -667,11 +675,36 @@ public class ProjectController extends BaseController {
     }
   }
 
+  static class SubmapConnection {
+    @JsonSerialize(using = MinifiedBioEntitySerializer.class)
+    public BioEntity from;
+    @JsonSerialize(using = ModelDataAsModelIdSerializer.class)
+    public ModelData to;
+    
+    public SubmapConnection(Element element) {
+      from = element;
+      to = element.getSubmodel().getSubmodel();
+    }
+  }
+  
   @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
   @GetMapping(value = "/{projectId}/submapConnections")
-  public List<Map<String, Object>> getSubmapConnections(@PathVariable(value = "projectId") String projectId)
+  public List<SubmapConnection> getSubmapConnections(@PathVariable(value = "projectId") String projectId)
       throws QueryException {
-    return projectController.getSubmapConnections(projectId);
+    Project project = getProject(projectId);
+    Map<ElementProperty, List<? extends Object>> properties = new HashMap<>();
+    properties.put(ElementProperty.PROJECT, Arrays.asList(project));
+    properties.put(ElementProperty.SUBMAP_CONNECTION, Arrays.asList(Boolean.TRUE));
+
+    List<Element> elements = elementService.getElementsByFilter(properties, true);
+
+    List<SubmapConnection> result = new ArrayList<>();
+    for (Element element : elements) {
+      if (element.getSubmodel() != null) {
+        result.add(new SubmapConnection(element));
+      }
+    }
+    return result;
   }
 
   @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId) "

rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java

@@ -44,30 +44,5 @@ public class ProjectRestImpl extends BaseRestImpl {
     return project;
   }
 
-  public List<Map<String, Object>> getSubmapConnections(String projectId) throws QueryException {
-    Project project = getProjectByProjectId(projectId);
-    Map<ElementProperty, List<? extends Object>> properties = new HashMap<>();
-    properties.put(ElementProperty.PROJECT, Arrays.asList(project));
-    properties.put(ElementProperty.SUBMAP_CONNECTION, Arrays.asList(Boolean.TRUE));
-
-    List<Element> elements = elementService.getElementsByFilter(properties);
-
-    List<Map<String, Object>> result = new ArrayList<>();
-    for (Element element : elements) {
-      if (element.getSubmodel() != null) {
-        result.add(submodelConnectionToMap(element));
-      }
-    }
-    return result;
-  }
-
-  private Map<String, Object> submodelConnectionToMap(Element element) {
-    Map<String, Object> result = new TreeMap<>();
-    result.put("from", super.createMinifiedSearchResult(element));
-    Map<String, Object> to = new TreeMap<>();
-    to.put("modelId", element.getSubmodel().getSubmodel().getId());
-    result.put("to", to);
-    return result;
-  }
 
 }

rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java

@@ -21,10 +21,10 @@ import lcsb.mapviewer.annotation.services.TaxonomyBackend;
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.annotation.services.dapi.ChemicalSearchException;
 import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ElementIdentifierType;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.modelutils.serializer.model.map.ElementIdentifierType;
 import lcsb.mapviewer.services.ObjectNotFoundException;
 import lcsb.mapviewer.services.QueryException;
 import lcsb.mapviewer.services.interfaces.IElementService;

rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentController.java

@@ -19,6 +19,7 @@ import lcsb.mapviewer.api.*;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.model.security.PrivilegeType;
 import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.modelutils.serializer.model.map.ElementIdentifierType;
 import lcsb.mapviewer.services.QueryException;
 import lcsb.mapviewer.services.interfaces.IUserService;
 

rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java

@@ -11,7 +11,6 @@ import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
 import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ElementIdentifierType;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.geometry.PointTransformation;
 import lcsb.mapviewer.model.Project;
@@ -21,6 +20,7 @@ import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.modelutils.serializer.model.map.ElementIdentifierType;
 import lcsb.mapviewer.persist.dao.map.ReactionDao;
 import lcsb.mapviewer.persist.dao.map.species.ElementDao;
 import lcsb.mapviewer.services.ObjectNotFoundException;

rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java

@@ -12,10 +12,10 @@ import lcsb.mapviewer.annotation.data.Drug;
 import lcsb.mapviewer.annotation.services.DrugSearchException;
 import lcsb.mapviewer.annotation.services.TaxonomyBackend;
 import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ElementIdentifierType;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.modelutils.serializer.model.map.ElementIdentifierType;
 import lcsb.mapviewer.services.ObjectNotFoundException;
 import lcsb.mapviewer.services.QueryException;
 import lcsb.mapviewer.services.interfaces.IElementService;

rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java

@@ -12,10 +12,10 @@ import lcsb.mapviewer.annotation.data.MiRNA;
 import lcsb.mapviewer.annotation.services.MiRNASearchException;
 import lcsb.mapviewer.annotation.services.TaxonomyBackend;
 import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ElementIdentifierType;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.modelutils.serializer.model.map.ElementIdentifierType;
 import lcsb.mapviewer.services.ObjectNotFoundException;
 import lcsb.mapviewer.services.QueryException;
 import lcsb.mapviewer.services.interfaces.IElementService;

rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java

@@ -13,7 +13,6 @@ import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
 import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.api.ElementIdentifierType;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.geometry.ColorParser;
 import lcsb.mapviewer.model.Project;
@@ -24,6 +23,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.overlay.*;
 import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.modelutils.serializer.model.map.ElementIdentifierType;
 import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
 import lcsb.mapviewer.services.ObjectNotFoundException;
 import lcsb.mapviewer.services.QueryException;

rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java

@@ -18,7 +18,7 @@ import lcsb.mapviewer.api.projects.overlays.OverlayRestImplTest;
     AllMiRnaTests.class,
     AllModelsTests.class,
     OverlayRestImplTest.class,
-    ProjectRestImplTest.class })
+    ProjectControllerTest.class })
 public class AllProjectTests {
 
 }

rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java

-package lcsb.mapviewer.api.projects;
-
-import static org.junit.Assert.assertEquals;
-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.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.api.RestTestFunctions;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.ProjectLogEntry;
-import lcsb.mapviewer.model.ProjectLogEntryType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.persist.dao.user.UserDao;
-import lcsb.mapviewer.services.ObjectNotFoundException;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IProjectService;
-
-public class ProjectRestImplTest extends RestTestFunctions {
-  Logger logger = LogManager.getLogger();
-
-  @Autowired
-  ProjectRestImpl _projectRest;
-
-  ProjectRestImpl projectRest;
-
-  @Autowired
-  IModelService modelService;
-
-  @Autowired
-  IProjectService projectService;
-
-  @Autowired
-  ProjectDao projectDao;
-
-  @Autowired
-  UserDao userDao;
-
-  @Before
-  public void before() {
-    projectRest = _projectRest;
-  }
-
-  @Test(expected = ObjectNotFoundException.class)
-  public void testGetInvalidMetaData() throws Exception {
-    projectRest.getProject("unknown_model_id");
-  }
-
-  private void createMockProjectRest(String string) throws Exception {
-    Model model = null;
-    Project project = null;
-    model = super.getModelForFile(string, false);
-    project = new Project(model.getName());
-    project.addModel(model);
-    project.setOwner(userDao.getUserByLogin(ADMIN_BUILT_IN_LOGIN));
-    project.setProjectId(model.getName());
-    ProjectLogEntry entry = new ProjectLogEntry();
-    entry.setContent("content");
-    entry.setType(ProjectLogEntryType.OTHER);
-    entry.setSeverity("DEBUG");
-    project.addLogEntry(entry);
-    projectDao.add(project);
-    projectRest = Mockito.spy(_projectRest);
-  }
-
-}

service/src/main/java/lcsb/mapviewer/services/impl/ElementService.java

@@ -2,6 +2,7 @@ package lcsb.mapviewer.services.impl;
 
 import java.util.*;
 
+import org.hibernate.Hibernate;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
@@ -82,4 +83,16 @@ public class ElementService implements IElementService {
     return elementAnnotations;
   }
 
+  @Override
+  public List<Element> getElementsByFilter(Map<ElementProperty, List<? extends Object>> properties, boolean initializeLazy) {
+    List<Element> result = getElementsByFilter(properties);
+    if (initializeLazy) {
+      for (Element element : result) {
+        Hibernate.initialize(element.getSubmodel().getSubmodel());
+        Hibernate.initialize(element.getModel());
+      }
+    }
+    return result;
+  }
+
 }

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

@@ -18,6 +18,8 @@ public interface IElementService {
   Element getElementById(String projectId, int mapId, int elementId) throws QueryException;
 
   List<Element> getElementsByFilter(Map<ElementProperty, List<? extends Object>> properties);
+  
+  List<Element> getElementsByFilter(Map<ElementProperty, List<? extends Object>> properties, boolean initializeLazy);
 
   Map<MiriamType, Integer> getAnnotationStatistics(String projectId, String mapId) throws QueryException;
 

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

@@ -35,7 +35,6 @@ import org.springframework.test.web.servlet.RequestBuilder;
 
 import com.google.gson.JsonParser;
 
-import lcsb.mapviewer.api.ElementIdentifierType;
 import lcsb.mapviewer.api.projects.comments.CommentRestImpl;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.model.Project;
@@ -45,6 +44,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.security.PrivilegeType;
 import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.modelutils.serializer.model.map.ElementIdentifierType;
 import lcsb.mapviewer.persist.dao.map.CommentDao;
 import lcsb.mapviewer.services.interfaces.ICommentService;
 import lcsb.mapviewer.services.interfaces.IUserService;

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

@@ -369,6 +369,7 @@ abstract public class ControllerIntegrationTest {
 
     ModelSubmodelConnection submodelConnection = new ModelSubmodelConnection(submap, SubmodelType.UNKNOWN);
     map.addSubmodel(submodelConnection);
+    element.setSubmodel(new ElementSubmodelConnection(submap, SubmodelType.UNKNOWN));
 
     project.addModel(map);
     project.addModel(submap);

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

@@ -31,7 +31,6 @@ import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.gson.JsonParser;
 
-import lcsb.mapviewer.api.ElementIdentifierType;
 import lcsb.mapviewer.api.projects.models.bioEntities.elements.ElementsRestImpl;
 import lcsb.mapviewer.api.projects.models.bioEntities.reactions.ReactionsRestImpl;
 import lcsb.mapviewer.common.Configuration;
@@ -47,6 +46,7 @@ import lcsb.mapviewer.model.overlay.DataOverlay;
 import lcsb.mapviewer.model.security.PrivilegeType;
 import lcsb.mapviewer.model.user.User;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
+import lcsb.mapviewer.modelutils.serializer.model.map.ElementIdentifierType;
 import lcsb.mapviewer.services.interfaces.IUserService;
 
 @RunWith(SpringJUnit4ClassRunner.class)

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

@@ -510,15 +510,22 @@ public class ProjectControllerIntegrationTest extends ControllerIntegrationTest
 
   @Test
   public void testGetSubmapConnectionsForProject() throws Exception {
+    createProjectInSeparateThread(TEST_PROJECT);
+
     MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
 
-    RequestBuilder request = get("/api/projects/{projectId}/submapConnections/", BUILT_IN_PROJECT).session(session);
+    RequestBuilder request = get("/api/projects/{projectId}/submapConnections/", TEST_PROJECT).session(session);
 
     mockMvc.perform(request)
         .andExpect(status().is2xxSuccessful())
         .andDo(document("projects/project_maps/get_connections",
             projectPathParameters(),
-            responseFields(fieldWithPath("[]").description("list of connections").type("array"))));
+            responseFields(
+                fieldWithPath("[]").description("list of connections").type(JsonFieldType.ARRAY),
+                fieldWithPath("[].from.id").description("anchor bioEntity id").type(JsonFieldType.NUMBER),
+                fieldWithPath("[].from.modelId").description("anchor map id").type(JsonFieldType.NUMBER),
+                fieldWithPath("[].from.type").description("anchor type").type(JsonFieldType.STRING),
+                fieldWithPath("[].to.modelId").description("destination map id").type(JsonFieldType.NUMBER))));
   }
 
   @Test