Merge branch '1230-comments-in-submap' into 'devel_14.0.x'

Resolve "in submap the comment's bubble is not displayed"

See merge request !1119

CHANGELOG

+minerva (14.0.12) stable; urgency=medium
+  * Bug fix: comments on submaps were not visible (#1230)
+  * Bug fix: removing comment from submap did not work
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 11 May 2020 17:00:00 +0200
+
 minerva (14.0.11) stable; urgency=medium
   * Bug fix: complex with no border was inproperly imported from CellDesigner 
     (#1198)

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java

@@ -35,7 +35,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
   /**
    * Version of the rest API that is supported by this annotator.
    */
-  static final String SUPPORTED_VERSION = "11.2";
+  static final String SUPPORTED_VERSION = "12.0";
 
   /**
    * Url address of ensembl restful service.

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

@@ -47,6 +47,7 @@ public class CommentController extends BaseController {
       Authentication authentication,
       @PathVariable(value = "projectId") String projectId,
       @RequestParam(value = "columns", defaultValue = "") String columns,
+      @PathVariable(value = "modelId") String modelId,
       @RequestParam(value = "removed", defaultValue = "") String removed) throws QueryException {
     boolean isAdmin = authentication.getAuthorities()
         .contains(new SimpleGrantedAuthority(PrivilegeType.IS_ADMIN.name()));
@@ -56,7 +57,7 @@ public class CommentController extends BaseController {
             .contains(new SimpleGrantedAuthority(PrivilegeType.READ_PROJECT.name() + ":" + projectId));
 
     List<Map<String, Object>> comments = commentController.getCommentList(
-        projectId, columns, "", "", removed);
+        projectId, columns, "", "", removed, modelId);
     if (!isAdmin && !isProjectCurator) {
       comments.forEach(comment -> {
         comment.remove("author");
@@ -89,10 +90,11 @@ public class CommentController extends BaseController {
   public List<Map<String, Object>> getCommentsByReaction(
       @PathVariable(value = "projectId") String projectId,
       @RequestParam(value = "columns", defaultValue = "") String columns,
+      @PathVariable(value = "modelId") String modelId,
       @PathVariable(value = "reactionId") String reactionId,
       @RequestParam(value = "removed", defaultValue = "") String removed) throws QueryException {
     return commentController.getCommentList(projectId, columns, reactionId,
-        ElementIdentifierType.REACTION.getJsName(), removed);
+        ElementIdentifierType.REACTION.getJsName(), removed, modelId);
   }
 
   @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
@@ -105,9 +107,10 @@ public class CommentController extends BaseController {
       @PathVariable(value = "projectId") String projectId,
       @RequestParam(value = "columns", defaultValue = "") String columns,
       @PathVariable(value = "elementId") String elementId,
+      @PathVariable(value = "modelId") String modelId,
       @RequestParam(value = "removed", defaultValue = "") String removed) throws QueryException {
     return commentController.getCommentList(
-        projectId, columns, elementId, ElementIdentifierType.ALIAS.getJsName(), removed);
+        projectId, columns, elementId, ElementIdentifierType.ALIAS.getJsName(), removed, modelId);
   }
 
   @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
@@ -120,9 +123,10 @@ public class CommentController extends BaseController {
       @PathVariable(value = "projectId") String projectId,
       @RequestParam(value = "columns", defaultValue = "") String columns,
       @PathVariable(value = "coordinates") String coordinates,
+      @PathVariable(value = "modelId") String modelId,
       @RequestParam(value = "removed", defaultValue = "") String removed) throws QueryException {
     return commentController.getCommentList(projectId, columns, coordinates,
-        ElementIdentifierType.POINT.getJsName(), removed);
+        ElementIdentifierType.POINT.getJsName(), removed, modelId);
   }
 
   @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")

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

@@ -15,7 +15,7 @@ import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.geometry.PointTransformation;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.*;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.user.User;
@@ -49,7 +49,7 @@ public class CommentRestImpl extends BaseRestImpl {
 
   public List<Map<String, Object>> getCommentList(
       String projectId, String columns, String elementId,
-      String elementType, String removed) throws QueryException {
+      String elementType, String removed, String modelId) throws QueryException {
     Project project = getProjectService().getProjectByProjectId(projectId);
     if (project == null) {
       throw new ObjectNotFoundException("Project with given id doesn't exist");
@@ -58,7 +58,9 @@ public class CommentRestImpl extends BaseRestImpl {
 
     List<Map<String, Object>> result = new ArrayList<>();
 
-    List<Comment> comments = commentService.getCommentsByProject(project);
+    List<Model> models = super.getModels(projectId, modelId);
+
+    List<Comment> comments = commentService.getCommentsByModel(models);
     for (Comment comment : comments) {
       boolean reject = false;
       if (!"".equals(elementType)) {
@@ -246,7 +248,8 @@ public class CommentRestImpl extends BaseRestImpl {
   }
 
   public Map<String, Object> addComment(String projectId, String elementType, String elementId,
-      String name, String email, String content, boolean pinned, Point2D pointCoordinates, String submodelId, User owner)
+      String name, String email, String content, boolean pinned, Point2D pointCoordinates, String submodelId,
+      User owner)
       throws QueryException {
     Model model = getModelService().getLastModelByProjectId(projectId);
     if (model == null) {
@@ -292,9 +295,26 @@ public class CommentRestImpl extends BaseRestImpl {
       throw new ObjectNotFoundException("Project with given id doesn't exist");
     }
     Comment comment = commentService.getCommentById(commentId);
-    if (comment == null || comment.getModelData().getProject().getId() != project.getId()) {
+
+    if (comment == null) {
+      throw new ObjectNotFoundException("Comment with given id doesn't exist");
+    }
+    if (comment.getModelData().getProject() != null && comment.getModelData().getProject().getId() != project.getId()) {
       throw new ObjectNotFoundException("Comment with given id doesn't exist");
     }
+    boolean isSubmap = false;
+    if (comment.getModelData().getProject() == null) {
+      for (ModelData model : project.getModels()) {
+        for (ModelSubmodelConnection submodel : model.getSubmodels()) {
+          if (submodel.getSubmodel().getId().equals(comment.getModelData().getId())) {
+            isSubmap = true;
+          }
+        }
+      }
+      if (!isSubmap) {
+        throw new ObjectNotFoundException("Comment with given id doesn't exist");
+      }
+    }
 
     commentService.deleteComment(comment, reason);
     return okStatus();

rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/CommentRestImplTest.java

@@ -37,14 +37,7 @@ public class CommentRestImplTest extends RestTestFunctions {
 
   @Test(expected = QueryException.class)
   public void testGetForNonExisting() throws Exception {
-    _commentRestImpl.getCommentList("unk", "", "", "", "");
-  }
-
-  @Test
-  public void testGetCommentsDependencies() throws Exception {
-    CommentRestImpl commentRestImpl = createMockProjectRest("testFiles/model/sample.xml");
-    commentRestImpl.getCommentList("sample", "", "", "", "");
-    Mockito.verify(commentRestImpl.getModelService(), times(0)).getLastModelByProjectId(anyString());
+    _commentRestImpl.getCommentList("unk", "", "", "", "", "*");
   }
 
   private CommentRestImpl createMockProjectRest(String string) throws Exception {

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

@@ -140,9 +140,9 @@ public class CommentService implements ICommentService {
   }
 
   @Override
-  public List<Comment> getCommentsByProject(Project project) {
+  public List<Comment> getCommentsByModel(List<Model> models) {
     List<Comment> comments = new ArrayList<>();
-    for (ModelData model : project.getModels()) {
+    for (Model model : models) {
       List<Comment> modelComments = commentDao.getCommentByModel(model, null, null);
       comments.addAll(modelComments);
     }

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

@@ -55,7 +55,7 @@ public interface ICommentService {
 
   void deleteComment(Comment comment, String reason);
 
-  List<Comment> getCommentsByProject(Project project);
+  List<Comment> getCommentsByModel(List<Model> models);
 
   /**
    * Returns number of comments in the system.

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

@@ -4,7 +4,6 @@ import static org.junit.Assert.*;
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
 
-import java.awt.geom.Point2D;
 import java.util.Arrays;
 
 import org.apache.http.client.entity.UrlEncodedFormEntity;
@@ -86,7 +85,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
 
     createComments();
 
-    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getIdModel() + "/")
+    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getId() + "/")
         .contentType(MediaType.APPLICATION_FORM_URLENCODED)
         .session(session);
 
@@ -107,7 +106,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
 
     createComments();
 
-    RequestBuilder request = get("/projects/*/comments/models/" + map.getIdModel() + "/")
+    RequestBuilder request = get("/projects/*/comments/models/" + map.getId() + "/")
         .contentType(MediaType.APPLICATION_FORM_URLENCODED)
         .session(session);
 
@@ -124,7 +123,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
 
     createComments();
 
-    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getIdModel() + "/")
+    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getId() + "/")
         .contentType(MediaType.APPLICATION_FORM_URLENCODED)
         .session(session);
 
@@ -159,7 +158,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
 
     createComments();
 
-    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getIdModel() + "/")
+    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getId() + "/")
         .contentType(MediaType.APPLICATION_FORM_URLENCODED)
         .session(session);
 
@@ -184,7 +183,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
     comment.setPinned(true);
     commentDao.add(comment);
 
-    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getIdModel() + "/")
+    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getId() + "/")
         .contentType(MediaType.APPLICATION_FORM_URLENCODED)
         .session(session);
 
@@ -209,7 +208,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
     comment.setPinned(true);
     commentDao.add(comment);
 
-    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getIdModel() + "/")
+    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getId() + "/")
         .contentType(MediaType.APPLICATION_FORM_URLENCODED)
         .session(session);
 
@@ -234,7 +233,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
     comment.setPinned(true);
     commentDao.add(comment);
 
-    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getIdModel() + "/")
+    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getId() + "/")
         .contentType(MediaType.APPLICATION_FORM_URLENCODED)
         .session(session);
 
@@ -256,7 +255,7 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
 
     createComments();
 
-    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getIdModel() + "/")
+    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/" + map.getId() + "/")
         .contentType(MediaType.APPLICATION_FORM_URLENCODED)
         .session(session);
 
@@ -874,6 +873,45 @@ public class CommentControllerIntegrationTest extends ControllerIntegrationTest
         .andExpect(status().isNotFound());
   }
 
+  @Test
+  public void testCommentsOnNonExistingModel() throws Exception {
+    createAdmin(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
+
+    MockHttpSession session = createSession(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
+
+    createComments();
+
+    RequestBuilder request = get("/projects/" + TEST_PROJECT + "/comments/models/0/")
+        .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+        .session(session);
+
+    mockMvc.perform(request)
+        .andExpect(status().isNotFound());
+  }
+
+  @Test
+  public void testRemoveFromSubmap() throws Exception {
+    createAdmin(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
+
+    MockHttpSession session = createSession(TEST_ADMIN_LOGIN, TEST_ADMIN_PASSWORD);
+
+    ModelData submap = map.getSubmodels().iterator().next().getSubmodel();
+    
+    Comment comment = createComment(submap);
+    commentDao.add(comment);
+
+    RequestBuilder request = delete("/projects/" + TEST_PROJECT + "/comments/" + comment.getId() + "/")
+        .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+        .session(session);
+
+    mockMvc.perform(request)
+        .andExpect(status().is2xxSuccessful());
+
+    assertEquals(true, comment.isDeleted());
+  }
+
+
+  
   private Comment createReactionComment() {
     Comment comment = createComment(map);
     comment.setTableName(reaction.getClass());

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

@@ -38,7 +38,7 @@ import lcsb.mapviewer.model.map.Comment;
 import lcsb.mapviewer.model.map.layout.ColorSchemaType;
 import lcsb.mapviewer.model.map.layout.Layout;
 import lcsb.mapviewer.model.map.layout.graphics.Glyph;
-import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.*;
 import lcsb.mapviewer.model.map.reaction.*;
 import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
 import lcsb.mapviewer.model.map.species.Element;
@@ -248,6 +248,15 @@ abstract public class ControllerIntegrationTest {
     product.setLine(new PolylineData(new Point2D.Double(10, 0), new Point2D.Double(20, 0)));
     reaction.addProduct(product);
 
+    ModelData submap = new ModelData();
+    submap.setTileSize(256);
+    submap.setWidth(100);
+    submap.setHeight(100);
+    
+    ModelSubmodelConnection submodelConnection = new ModelSubmodelConnection(submap, SubmodelType.UNKNOWN);
+    map.addSubmodel(submodelConnection);
+
+    
     project.addModel(map);
     projectDao.add(project);
     return project;