Merge branch '780-login-with-problematic-characters' into 'devel_12.2.x'

Resolve "MINERVANET - Error Report 57"

See merge request !727

CHANGELOG

@@ -3,6 +3,10 @@ minerva (12.2.2) stable; urgency=medium
     with different id than default map was accessed
   * Bug fix: change of owner of the data overlay in admin panel incorrectly 
     ordered overlays (#777)
+  * Bug fix: chemical search didn't use updated disease identifier, original 
+    disease id from project upload was used instead (#779)
+  * Bug fix: user login with special characters (like '@')  could cause 
+    problems in admin panel (#780)
 
 minerva (12.2.1) stable; urgency=medium
   * Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can

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

@@ -1017,8 +1017,6 @@ EditProjectDialog.prototype.saveOverlay = function (overlayId) {
     overlay.setCreator(creator);
     overlay.setOrder(order);
   }
-  console.log("output");
-  console.log(overlay);
   return self.getServerConnector().updateOverlay(overlay);
 };
 

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

@@ -299,7 +299,7 @@ UsersAdminPanel.prototype.addUpdateListener = function (user, dataTableRow) {
     }
   }
   var listener = function () {
-    var login = user.getLogin().replace(".", "\\.");
+    var login = $.escapeSelector(user.getLogin());
     self.userToTableRow(user, dataTableRow);
     var row = $($("[name='usersTable']", self.getElement())[0]).DataTable().row("#" + login);
     if (row.length > 0) {

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

@@ -102,6 +102,18 @@ describe('UsersAdminPanel', function () {
     });
   });
 
+  it('onUpdateUserListener', function () {
+    helper.loginAsAdmin();
+    var usersTab = createUserAdminPanel();
+    return usersTab.init().then(function () {
+      var user = helper.createUser();
+      user.setLogin("x@y.lu");
+      var data = [];
+      usersTab.addUpdateListener(user, data);
+      user.callListeners("onreload");
+      assert.ok(data.indexOf("x@y.lu") >= 0);
+      return usersTab.destroy();
+    });
+  });
 
-})
-;
+});

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

@@ -58,7 +58,7 @@ public class ChemicalRestImpl extends BaseRestImpl {
     if (model == null) {
       throw new QueryException("Project with given id doesn't exist");
     }
-    Project project = model.getProject();
+    Project project = getProjectService().getProjectByProjectId(projectId, token);
     if (project.getDisease() == null) {
       throw new QueryException("Project doesn't have disease associated to it");
     }
@@ -175,7 +175,7 @@ public class ChemicalRestImpl extends BaseRestImpl {
     if (model == null) {
       throw new QueryException("Project with given id doesn't exist");
     }
-    Project project = model.getProject();
+    Project project = getProjectService().getProjectByProjectId(projectId, token);
 
     if (project.getDisease() == null) {
       throw new QueryException("Project doesn't have disease associated to it");

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

@@ -54,7 +54,7 @@ public class DrugRestImpl extends BaseRestImpl {
     if (model == null) {
       throw new QueryException("Project with given id doesn't exist");
     }
-    Project project = model.getProject();
+    Project project = getProjectService().getProjectByProjectId(projectId, token);
 
     Set<String> columnSet = createDrugColumnSet(columns);
 
@@ -160,7 +160,7 @@ public class DrugRestImpl extends BaseRestImpl {
     if (model == null) {
       throw new QueryException("Project with given id doesn't exist");
     }
-    Project project = model.getProject();
+    Project project = getProjectService().getProjectByProjectId(projectId, token);
 
     List<Model> models = getModels(projectId, "*", token);
 

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

@@ -53,7 +53,7 @@ public class MiRnaRestImpl extends BaseRestImpl {
     if (model == null) {
       throw new QueryException("Project with given id doesn't exist");
     }
-    Project project = model.getProject();
+    Project project = getProjectService().getProjectByProjectId(projectId, token);
 
     Set<String> columnSet = createMiRnaColumnSet(columns);
 
@@ -129,7 +129,7 @@ public class MiRnaRestImpl extends BaseRestImpl {
     if (model == null) {
       throw new QueryException("Project with given id doesn't exist");
     }
-    Project project = model.getProject();
+    Project project = getProjectService().getProjectByProjectId(projectId, token);
 
     List<Model> models = getModels(projectId, "*", token);
 

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

 package lcsb.mapviewer.api;
 
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileInputStream;
@@ -32,6 +35,7 @@ import org.apache.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.runner.RunWith;
+import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.security.crypto.password.PasswordEncoder;
 import org.springframework.test.annotation.Rollback;
@@ -46,6 +50,7 @@ import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
 import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.ComplexZipConverter;
 import lcsb.mapviewer.converter.ComplexZipConverterParams;
@@ -59,6 +64,8 @@ import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
 import lcsb.mapviewer.model.map.model.SubmodelType;
 import lcsb.mapviewer.persist.DbUtils;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
 import lcsb.mapviewer.services.interfaces.IUserService;
 
 @Transactional
@@ -312,4 +319,21 @@ public abstract class RestTestFunctions {
     return tmp.toString();
   }
 
+  protected IProjectService createProjectMockServiceForModel(Model model) {
+    try {
+      IProjectService mockModelService = Mockito.mock(IProjectService.class);
+      Mockito.when(mockModelService.getProjectByProjectId(anyString(), anyString())).thenReturn(model.getProject());
+      return mockModelService;
+    } catch (lcsb.mapviewer.services.SecurityException e) {
+      throw new InvalidStateException(e);
+    }
+  }
+
+  protected IModelService createModelMockServiceForModel(Model model) throws lcsb.mapviewer.services.SecurityException {
+    IModelService mockModelService = Mockito.mock(IModelService.class);
+    Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+    return mockModelService;
+  }
+
+
 }

rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java

 package lcsb.mapviewer.api.projects.drugs;
 
 import static org.junit.Assert.assertNotNull;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
 
 import java.util.List;
 import java.util.Map;
@@ -16,8 +16,11 @@ import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.SecurityException;
 import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
 
 public class DrugRestImplTest extends RestTestFunctions {
   Logger logger = Logger.getLogger(DrugRestImplTest.class);
@@ -53,7 +56,7 @@ public class DrugRestImplTest extends RestTestFunctions {
       throw e;
     }
   }
-  
+
   @Test
   public void testTargetWithEmptyMechanism() throws Exception {
     try {
@@ -69,9 +72,8 @@ public class DrugRestImplTest extends RestTestFunctions {
 
   private DrugRestImpl createMockProjectRest(String string) throws Exception {
     Model model = super.getModelForFile(string, true);
-    IModelService mockModelService = Mockito.mock(IModelService.class);
-    Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
-    _drugRestImpl.setModelService(mockModelService);
+    _drugRestImpl.setModelService(createModelMockServiceForModel(model));
+    _drugRestImpl.setProjectService(createProjectMockServiceForModel(model));
     return _drugRestImpl;
   }
 

rest-api/src/test/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImplTest.java

@@ -58,9 +58,8 @@ public class MiRnaRestImplTest extends RestTestFunctions {
 
   private MiRnaRestImpl createMockProjectRest(String string) throws Exception {
     Model model = super.getModelForFile(string, true);
-    IModelService mockModelService = Mockito.mock(IModelService.class);
-    Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
-    _miRnaRestImpl.setModelService(mockModelService);
+    _miRnaRestImpl.setModelService(createModelMockServiceForModel(model));
+    _miRnaRestImpl.setProjectService(createProjectMockServiceForModel(model));
     return _miRnaRestImpl;
   }
 

rest-api/src/test/resources/log4j.properties

@@ -19,4 +19,7 @@ log4j.logger.org.springframework=warn
 log4j.logger.org.hibernate=warn
 log4j.logger.lcsb=debug
 log4j.logger.lcsb.mapviewer.annotation.cache=info
-log4j.logger.lcsb.mapviewer.persist=info
\ No newline at end of file
+log4j.logger.lcsb.mapviewer.persist=info
+
+#There are plenty of useless warnings in jsbml library
+log4j.logger.org.sbml.jsbml=error
\ No newline at end of file