Merge branch 'devel_12.1.x' into HEAD

CHANGELOG

@@ -7,6 +7,20 @@ minerva (12.2.0~alpha.0) stable; urgency=medium
     highligh
 
 
+minerva (12.1.4) stable; urgency=medium
+  * Bug fix: no check for limit on custom data overlays fixed
+  * Bug fix: error message improved when there is privilege problem during
+    data overlay upload
+  * Bug fix: upload of data overlay from admin panel didn't work
+  * Bug fix: add project button is disabled when user doesn't have proper
+    privileges ("Add project" privilege)
+  * Bug fix: there are no more extra markers due to map wrapping
+  * Bug fix: upload of the project failed when another project was removed
+    during upload
+  * Bug fix:  word wrapping fixed in overlay table for long overlay names
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 28 Dec 2018 14:00:00 +0200
+
 minerva (12.1.3) stable; urgency=medium
   * Bug fix: add project button is disabled when user has no privileges
   * Bug fix: projectId was missing in the edit window

frontend-js/src/main/css/global.css

@@ -926,6 +926,10 @@ https://www.w3schools.com/css/tryit.asp?filename=trycss_tooltip
     overflow-x: hidden;
 }
 
+.minerva-overlay-panel td, .minerva-overlay-panel th {
+    word-break: break-word;
+}
+
 .minerva-search-data-hidden {
     display: none;
 }

frontend-js/src/main/js/ServerConnector.js

@@ -2165,7 +2165,7 @@ ServerConnector.addOverlay = function (params) {
     return self.sendPostRequest(self.addOverlayUrl(queryParams), data);
   }).then(function (content) {
     return new DataOverlay(JSON.parse(content));
-  });
+  }).catch(self.processNetworkError);
 };
 
 /**

frontend-js/src/main/js/gui/AddOverlayDialog.js

@@ -7,6 +7,7 @@ var GuiConnector = require('../GuiConnector');
 var GuiUtils = require('./leftPanel/GuiUtils');
 var DataOverlay = require('../map/data/DataOverlay');
 var NetworkError = require('../NetworkError');
+var SecurityError = require('../SecurityError');
 
 var OverlayParser = require('../map/OverlayParser');
 
@@ -295,6 +296,8 @@ AddOverlayDialog.prototype.open = function () {
             if (error instanceof NetworkError && error.statusCode === HttpStatus.BAD_REQUEST) {
               var errorMessage = JSON.parse(error.content);
               GuiConnector.alert("Problematic input: <br/>" + errorMessage.reason);
+            } else if (error instanceof SecurityError) {
+              GuiConnector.alert("You cannot add more overlays");
             } else {
               GuiConnector.alert(error);
             }

frontend-js/src/main/js/gui/admin/EditProjectDialog.js

@@ -1033,7 +1033,7 @@ EditProjectDialog.prototype.removeOverlay = function (overlayId) {
 
 /**
  *
- * @returns {Promise}
+ * @returns {Promise<AddOverlayDialog>}
  */
 EditProjectDialog.prototype.openAddOverlayDialog = function () {
   var self = this;
@@ -1044,13 +1044,16 @@ EditProjectDialog.prototype.openAddOverlayDialog = function () {
     project: self.getProject(),
     customMap: null,
     element: document.createElement("div"),
-    configuration: self.getConfiguration()
+    configuration: self.getConfiguration(),
+    serverConnector: self.getServerConnector()
   });
   self._addOverlayDialog.addListener("onAddOverlay", function () {
     return self.refreshOverlays();
   });
   return self._addOverlayDialog.init().then(function () {
     return self._addOverlayDialog.open();
+  }).then(function(){
+    return self._addOverlayDialog;
   });
 };
 

frontend-js/src/main/js/gui/admin/MapsAdminPanel.js

@@ -191,7 +191,7 @@ MapsAdminPanel.prototype.init = function () {
     return self.getServerConnector().getLoggedUser();
   }).then(function (user) {
     var configuration = self.getConfiguration();
-    var canAddProject = user.hasPrivilege(configuration.getPrivilegeType(PrivilegeType.PROJECT_MANAGEMENT));
+    var canAddProject = user.hasPrivilege(configuration.getPrivilegeType(PrivilegeType.ADD_MAP));
     $("[name='addProject']", self.getElement()).attr("disabled", !canAddProject);
   });
 };

frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerCanvas.js

@@ -26,24 +26,28 @@ function OpenLayerCanvas(element, options) {
 
   self._markerLayer = new ol.layer.Vector({
     source: new ol.source.Vector({
+      wrapX: false,
       features: []
     })
   });
 
   self._rectangleLayer = new ol.layer.Vector({
     source: new ol.source.Vector({
+      wrapX: false,
       features: []
     })
   });
 
   self._polylineLayer = new ol.layer.Vector({
     source: new ol.source.Vector({
+      wrapX: false,
       features: []
     })
   });
 
   self._drawingLayer = new ol.layer.Vector({
     source: new ol.source.Vector({
+      wrapX: false,
       features: []
     }),
     style: new ol.style.Style({

frontend-js/src/main/js/map/data/PrivilegeType.js

@@ -34,6 +34,7 @@ PrivilegeType.CONFIGURATION_MANAGE = 'CONFIGURATION_MANAGE';
 PrivilegeType.MANAGE_GENOMES = 'MANAGE_GENOMES';
 PrivilegeType.MANAGE_PLUGINS = 'MANAGE_PLUGINS';
 PrivilegeType.PROJECT_MANAGEMENT = 'PROJECT_MANAGEMENT';
+PrivilegeType.ADD_MAP = 'ADD_MAP';
 PrivilegeType.USER_MANAGEMENT = 'USER_MANAGEMENT';
 
 /**

frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js

@@ -122,8 +122,11 @@ describe('EditProjectDialog', function () {
     return createDialog().then(function (result) {
       dialog = result;
       return dialog.openAddOverlayDialog();
+    }).then(function (overlayDialog) {
+      overlayDialog.setFileContent("X");
+      return $("button:contains('UPLOAD')").click();
     }).then(function () {
-      dialog.destroy();
+      return dialog.destroy();
     });
   });
 

rest-api/src/test/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImplTest.java

@@ -13,6 +13,10 @@ import lcsb.mapviewer.api.RestTestFunctions;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.layout.ColorSchemaType;
 import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.user.ObjectPrivilege;
+import lcsb.mapviewer.model.user.Privilege;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
 import lcsb.mapviewer.persist.dao.ProjectDao;
 import lcsb.mapviewer.services.interfaces.IProjectService;
 
@@ -32,7 +36,11 @@ public class OverlayRestImplTest extends RestTestFunctions {
   @Test
   public void testAddDataOverlay() throws Exception {
     try {
-      createProject("testFiles/model/sample.xml", projectId);
+      User admin = userService.getUserByLogin("admin");
+      Project project = createProject("testFiles/model/sample.xml", projectId);
+      userService.setUserPrivilege(admin, new Privilege(100, PrivilegeType.CUSTOM_LAYOUTS, admin));
+      userService.setUserPrivilege(admin, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, admin));
+
       Map<String, Object> result = overlayRest.addOverlay(adminToken, projectId, "x", "desc", "s1", null, null,
           ColorSchemaType.GENERIC.name(), "true");
       Gson gson = new Gson();
@@ -45,11 +53,12 @@ public class OverlayRestImplTest extends RestTestFunctions {
     }
   }
 
-  private void createProject(String string, String projectId) throws Exception {
+  private Project createProject(String string, String projectId) throws Exception {
     Project project = new Project(projectId);
     Model model = super.getModelForFile(string, false);
     project.addModel(model);
     projectDao.add(project);
+    return project;
   }
 
 }

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

@@ -120,9 +120,9 @@ public class LayoutService implements ILayoutService {
     }
 
     @Override
-    public boolean userCanAddLayout(Model model, User user) {
+    public boolean userCanAddLayout(Project project, User user) {
         // if we don't have privileges to view the object then we cannot add layouts
-        if (!userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, model.getProject())) {
+        if (!userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, project)) {
             return false;
         }
         long count = getAvailableCustomLayoutsNumber(user);
@@ -394,7 +394,11 @@ public class LayoutService implements ILayoutService {
     }
 
   @Override
-  public Layout createLayout(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException {
+  public Layout createLayout(final CreateLayoutParams params)
+      throws IOException, InvalidColorSchemaException, SecurityException {
+    if (!userCanAddLayout(params.getProject(), params.getUser())) {
+      throw new SecurityException("You cannot add more overlays");
+    }
     ColorSchemaReader reader = new ColorSchemaReader();
     Map<String, String> parameters = TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream());
     if (parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) == null && params.getColorSchemaType() != null) {

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

@@ -754,6 +754,7 @@ public class ProjectService implements IProjectService {
 
           UploadedFileEntry file = params.getProjectFile();
           project.setInputData(file);
+          addUsers(project, params);
 
           createModel(params, project);
           Model originalModel = project.getModels().iterator().next().getModel();
@@ -764,7 +765,6 @@ public class ProjectService implements IProjectService {
                 .execute();
           }
 
-          addUsers(project, params);
           createImages(project, params);
 
           for (Layout layout : project.getLayouts()) {

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

@@ -309,14 +309,14 @@ public interface ILayoutService {
   /**
    * Returns true if user can add layout to the model.
    *
-   * @param model
-   *          to which model user wants to add layout
+   * @param project
+   *          to which project user wants to add layout
    * @param user
    *          who wants to add layout
    * @return <code>true</code> if user can add layout, <code>false</code>
    *         otherwise
    */
-  boolean userCanAddLayout(Model model, User user);
+  boolean userCanAddLayout(Project project, User user);
 
   /**
    * Returns true if user can remove layout from the model.
@@ -380,9 +380,10 @@ public interface ILayoutService {
    *           thrown when there are problems with files
    * @throws InvalidColorSchemaException
    *           if the coloring source is invalid
+   * @throws SecurityException 
    * @throws CommandExecutionException
    */
-  Layout createLayout(CreateLayoutParams params) throws IOException, InvalidColorSchemaException;
+  Layout createLayout(CreateLayoutParams params) throws IOException, InvalidColorSchemaException, SecurityException;
 
   /**
    * Create layout based on the data in the parameter. Layout will contain set of

service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java

@@ -130,14 +130,14 @@ public class LayoutServiceTest extends ServiceTestFunctions {
   public void testUserCanAddLayout() throws Exception {
     try {
       int initialSize = project.getLayouts().size();
-      assertFalse(layoutService.userCanAddLayout(model, user));
+      assertFalse(layoutService.userCanAddLayout(project, user));
       userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
 
-      assertFalse(layoutService.userCanAddLayout(model, user));
+      assertFalse(layoutService.userCanAddLayout(project, user));
 
       userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
 
-      assertTrue(layoutService.userCanAddLayout(model, user));
+      assertTrue(layoutService.userCanAddLayout(project, user));
 
       CreateLayoutParams params = new CreateLayoutParams().name("Test").
           directory("testDir").
@@ -146,15 +146,15 @@ public class LayoutServiceTest extends ServiceTestFunctions {
           user(user);
       Layout row = layoutService.createLayout(params);
 
-      assertFalse(layoutService.userCanAddLayout(model, user));
+      assertFalse(layoutService.userCanAddLayout(project, user));
 
       userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
 
-      assertFalse(layoutService.userCanAddLayout(model, user));
+      assertFalse(layoutService.userCanAddLayout(project, user));
 
       userService.setUserPrivilege(user, new Privilege(2, PrivilegeType.CUSTOM_LAYOUTS, user));
 
-      assertTrue(layoutService.userCanAddLayout(model, user));
+      assertTrue(layoutService.userCanAddLayout(project, user));
 
       assertTrue(layoutService.userCanRemoveLayout(row, user));
 
@@ -172,6 +172,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
   public void testGetAvailable() throws Exception {
     try {
       userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
+      userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
       assertEquals(1, layoutService.getAvailableCustomLayoutsNumber(user));
 
       CreateLayoutParams params = new CreateLayoutParams().name("Test").
@@ -201,6 +202,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
       assertEquals(0, layouts.size());
 
       userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
+      userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
 
       CreateLayoutParams params = new CreateLayoutParams().name("Test").
           directory("testDir").
@@ -235,6 +237,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
       assertEquals(0, layouts.size());
 
       userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
+      userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
 
       CreateLayoutParams params = new CreateLayoutParams().name("Test").
           directory("testDir").
@@ -271,6 +274,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
       assertEquals(0, layouts.size());
 
       userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
+      userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
       CreateLayoutParams params = new CreateLayoutParams().name("Test").
           directory("testDir").
           project(project).
@@ -371,6 +375,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
       assertEquals(0, layouts.size());
 
       userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
+      userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
       CreateLayoutParams params = new CreateLayoutParams().name("Test").
           directory("testDir").
           project(project).
@@ -404,6 +409,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
       assertEquals(0, layouts.size());
 
       userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
+      userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
       ByteArrayInputStream bais = new ByteArrayInputStream(
           "name	reactionIdentifier	Color\ns1		#CC0000\ns2		#CCCC00\n	re1	#CCCC00\n"
               .getBytes(StandardCharsets.UTF_8));
@@ -503,6 +509,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
     try {
       String layoutId = "Test";
       userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
+      userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
       CreateLayoutParams params = new CreateLayoutParams().name(layoutId).
           directory("testDir").
           project(project).
@@ -526,6 +533,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
     try {
       String layoutId = "Test";
       userService.setUserPrivilege(user, new Privilege(1, PrivilegeType.CUSTOM_LAYOUTS, user));
+      userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
       CreateLayoutParams params = new CreateLayoutParams().name(layoutId).
           directory("testDir").
           project(project).

service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java

@@ -59,6 +59,7 @@ import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Protein;
 import lcsb.mapviewer.model.user.ConfigurationElementType;
 import lcsb.mapviewer.model.user.ConfigurationOption;
+import lcsb.mapviewer.model.user.ObjectPrivilege;
 import lcsb.mapviewer.model.user.PrivilegeType;
 import lcsb.mapviewer.model.user.User;
 import lcsb.mapviewer.model.user.UserAnnotationSchema;
@@ -114,7 +115,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
   }
 
   @Test
-  public void test() throws Exception {
+  public void testGetAllProjects() throws Exception {
     try {
       List<Project> projects = projectService.getAllProjects(adminToken);
 
@@ -146,6 +147,73 @@ public class ProjectServiceTest extends ServiceTestFunctions {
     }
   }
 
+  @Test
+  public void testUserPrivilegeChangeDuringUpload() throws Exception {
+    try {
+      User admin = userService.getUserByToken(adminToken);
+      Project defaultProject = projectService.getAllProjects().get(0);
+      userService.setUserPrivilege(admin,
+          new ObjectPrivilege(defaultProject, 1, PrivilegeType.EDIT_COMMENTS_PROJECT, admin));
+      admin = userService.getUserByToken(adminToken);
+      String project_id = "test_id";
+      Thread addProjectThread = new Thread(new Runnable() {
+
+        @Override
+        public void run() {
+          try {
+            projectService.createProject(createProjectParams("testFiles/sample.xml").projectId(project_id));
+          } catch (Exception e) {
+            e.printStackTrace();
+          }
+        }
+      });
+      addProjectThread.start();
+
+      Thread dropPrivilegesThread = new Thread(new Runnable() {
+
+        @Override
+        public void run() {
+          try {
+            Thread.sleep(100);
+            userService.dropPrivilegesForObjectType(PrivilegeType.VIEW_PROJECT, defaultProject.getId());
+          } catch (Exception e) {
+            e.printStackTrace();
+          }
+        }
+      });
+
+      dropPrivilegesThread.start();
+      dropPrivilegesThread.join();
+
+      addProjectThread.join();
+
+      Project project = projectService.getProjectByProjectId(project_id, adminToken);
+      assertEquals(ProjectStatus.DONE, project.getStatus());
+      Thread removeProjectThread = new Thread(new Runnable() {
+
+        @Override
+        public void run() {
+          try {
+            Project project = projectService.getProjectByProjectId(project_id, adminToken);
+            assertEquals(ProjectStatus.DONE, project.getStatus());
+            projectService.removeProject(project, null, false, adminToken);
+          } catch (Exception e) {
+            e.printStackTrace();
+          }
+        }
+      });
+      removeProjectThread.start();
+
+      removeProjectThread.join();
+
+      assertNull(projectService.getProjectByProjectId(project_id, adminToken));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testUpdater() throws Exception {
     try {