Merge branch 'devel_12.2.x' into merge

CHANGELOG

@@ -38,6 +38,21 @@ minerva (12.3.0~alpha.0) unstable; urgency=low
   * Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is
     slightly separated from target phenotype (#664)
 
+minerva (12.2.2) stable; urgency=medium
+  * Bug fix: downloading overlays didn't work from admin panel when project
+    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)
+  * Bug fix: removing project without full control in the system (but with
+    enough privileges to remove project) caused "Not enough privileges" error
+    (#778)
+  * Bug fix: export of custom properties (like synonyms) are properly encoded
+    in CellDesigner xml (#785)
+
 minerva (12.2.1) stable; urgency=medium
   * Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can
     read colors properly) (#744)

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

@@ -9,6 +9,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
+import org.apache.commons.text.StringEscapeUtils;
 import org.apache.log4j.Logger;
 import org.springframework.stereotype.Service;
 import org.w3c.dom.Node;
@@ -263,7 +264,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
             Node node = list.item(i);
             if (node.getNodeType() == Node.ELEMENT_NODE) {
               if (node.getNodeName().equals("Gene-ref_syn_E")) {
-                synonyms.add(node.getTextContent());
+				synonyms.add(StringEscapeUtils.unescapeHtml4(node.getTextContent()));
               }
             }
           }

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java

@@ -271,6 +271,23 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testAnnotateElementWithEncodedSynonyms() throws Exception {
+    try {
+      Species proteinAlias = new GenericProtein("id");
+      proteinAlias.addMiriamData(new MiriamData(MiriamType.ENTREZ, "834106"));
+      entrezAnnotator.annotateElement(proteinAlias);
+
+      for (String synonym : proteinAlias.getSynonyms()) {
+        assertFalse("Invalid character found in synonym: " + synonym, synonym.contains("&"));
+      }
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testParseEntrezResponse() throws Exception {
     WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java

@@ -160,8 +160,9 @@ public class RestAnnotationParser {
         return "";
       }
     } else if (value instanceof String) {
-      if (!((String) value).trim().isEmpty() || forceFullInfo) {
-        return type.getCommonName() + ": " + value + "\n";
+      String string =(String) value; 
+      if (!(string.trim().isEmpty()) || forceFullInfo) {
+        return type.getCommonName() + ": " + XmlParser.escapeXml(string) + "\n";
       } else {
         return "";
       }
@@ -178,7 +179,7 @@ public class RestAnnotationParser {
           if (object instanceof MiriamData) {
             result += ((MiriamData) object).getResource();
           } else {
-            result += object;
+            result += XmlParser.escapeXml(object.toString());
           }
 
         }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java

@@ -59,6 +59,8 @@ import lcsb.mapviewer.model.map.species.Species;
 public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
   Logger logger = Logger.getLogger(CellDesignerXmlParserTest.class);
 
+  ModelComparator modelComparator = new ModelComparator();
+
   @Before
   public void setUp() throws Exception {
   }
@@ -447,8 +449,6 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
       InputStream is = new ByteArrayInputStream(xmlString.getBytes());
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
-      ModelComparator modelComparator = new ModelComparator();
-
       assertEquals(0, modelComparator.compare(model, model2));
 
     } catch (Exception e) {
@@ -1037,6 +1037,34 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
     }
   }
 
+  @Test
+  public void testSpeciesWithSpecialSynonym() throws Exception {
+    try {
+      Model model = new ModelFullIndexed(null);
+      model.setIdModel("as");
+      model.setWidth(10);
+      model.setHeight(10);
+      Species protein = new GenericProtein("id1");
+      protein.setWidth(10);
+      protein.setHeight(10);
+      protein.setName("ROS");
+      protein.addSynonym("&");
+      model.addElement(protein);
+
+      CellDesignerXmlParser parser = new CellDesignerXmlParser();
+      String xmlString = parser.model2String(model);
+      InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+      Model model2 = parser.createModel(new ConverterParams().inputStream(is));
+      
+      assertEquals(0, modelComparator.compare(model, model2));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testReactionCoordsEqual() throws Exception {
     try {

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

@@ -436,7 +436,8 @@ EditProjectDialog.prototype._createOverlayTable = function () {
   $(overlaysTable).on("click", "[name='downloadSource']", function () {
     var button = this;
     return self.getServerConnector().getOverlaySourceDownloadUrl({
-      overlayId: $(button).attr("data")
+      overlayId: $(button).attr("data"),
+      projectId:self.getProject().getProjectId()
     }).then(function (url) {
       return self.downloadFile(url);
     }).then(null, GuiConnector.alert);
@@ -990,8 +991,32 @@ EditProjectDialog.prototype.saveOverlay = function (overlayId) {
   overlay.setDescription($("[name='description-" + overlayId + "']", self.getElement())[0].value);
   overlay.setPublicOverlay($("[name='publicOverlay-" + overlayId + "']", self.getElement())[0].checked);
   overlay.setDefaultOverlay($("[name='defaultOverlay-" + overlayId + "']", self.getElement())[0].checked);
-  overlay.setCreator($("[name='creator-" + overlayId + "']", self.getElement())[0].value);
-
+  var creator = $("[name='creator-" + overlayId + "']", self.getElement())[0].value;
+  if (creator === "") {
+    creator = undefined;
+  }
+  if (overlay.getCreator() !== creator) {
+
+    //put it on the bottom of ordered list of data overlays for given user
+    var order = 1;
+    for (var key in self._overlayById) {
+      if (self._overlayById.hasOwnProperty(key)) {
+        var existingOverlay = self._overlayById[key];
+        if (existingOverlay.getCreator() === creator) {
+          if (existingOverlay.getId() !== overlayId) {
+            order = Math.max(order, self._overlayById[key].getOrder() + 1);
+          } else {
+            order = Math.max(order, self._overlayById[key].getOrder());
+          }
+        }
+      }
+    }
+    if (creator === undefined) {
+      creator = "";
+    }
+    overlay.setCreator(creator);
+    overlay.setOrder(order);
+  }
   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

@@ -53,7 +53,7 @@ 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);
 
@@ -159,7 +159,7 @@ 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;
@@ -33,6 +36,7 @@ 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;
@@ -47,6 +51,7 @@ 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.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
@@ -56,6 +61,8 @@ 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
@@ -309,4 +316,21 @@ 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/ProjectRestImplTest.java

@@ -33,6 +33,8 @@ import lcsb.mapviewer.converter.zip.ZipEntryFile;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
 import lcsb.mapviewer.persist.dao.ProjectDao;
 import lcsb.mapviewer.services.interfaces.IModelService;
 import lcsb.mapviewer.services.interfaces.IProjectService;
@@ -81,6 +83,24 @@ public class ProjectRestImplTest extends RestTestFunctions {
     }
   }
 
+  @Test
+  public void testRemoveProject() throws Exception {
+    try {
+      String projectId = "test";
+      Project project = new Project();
+      project.setProjectId(projectId);
+      projectDao.add(project);
+      User user = userService.getUserByToken(token);
+      userService.setUserPrivilege(user, PrivilegeType.VIEW_PROJECT,1, project.getId(), adminToken);
+      userService.setUserPrivilege(user, PrivilegeType.PROJECT_MANAGEMENT, 1);
+//      userService.setUserPrivilege(user, PrivilegeType.VIEW_PROJECT, 1);
+      _projectRestImpl.removeProject(token, projectId, null);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test(expected = ObjectNotFoundException.class)
   public void testGetInvalidMetaData() throws Exception {
     ProjectRestImpl projectRest = createMockProjectRest(null);

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

 package lcsb.mapviewer.api.projects.mirnas;
 
 import static org.junit.Assert.assertFalse;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
 
 import java.util.HashSet;
 import java.util.List;
@@ -14,12 +12,10 @@ import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Test;
-import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.api.RestTestFunctions;
 import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.services.interfaces.IModelService;
 
 public class MiRnaRestImplTest extends RestTestFunctions {
   Logger logger = Logger.getLogger(MiRnaRestImplTest.class);
@@ -58,9 +54,8 @@ 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

@@ -22,4 +22,4 @@ log4j.logger.lcsb.mapviewer.annotation.cache=info
 log4j.logger.lcsb.mapviewer.persist=info
 
 #There are plenty of useless warnings in jsbml library
-log4j.logger.org.sbml.jsbml=error
+log4j.logger.org.sbml.jsbml=error
\ No newline at end of file

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

@@ -298,7 +298,6 @@ public class ProjectService implements IProjectService {
         homeDir = null;
       }
     }
-    removePrivilegesForProject(p);
     updateProjectStatus(p, ProjectStatus.REMOVING, 0, new CreateProjectParams());
     Thread computations = new Thread(new Runnable() {
 
@@ -350,6 +349,7 @@ public class ProjectService implements IProjectService {
               }
             }
           }
+          removePrivilegesForProject(project);
           projectDao.delete(project);
           if (async) {
             projectDao.commit();